0.041768 0.000000 0.006805 0.000000 0.072717 0.000000 0.000000 0.000000 0.015805 0.000000 0.000000 0.000000 Whitby, F.G. Ratnitilakanabhuket, P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.000 99.250 90.000 23.942 13.752 64.106 C2 H4 O 44.053 ACETYL GROUP non-polymer C9 H10 N2 O4 210.187 n N-[(2-nitrophenyl)methyl]glycine 2-nitrobenzylglycine non-polymer C2 H5 N O2 75.067 y GLYCINE peptide linking H2 O 18.015 WATER non-polymer C5 H9 N O3 131.130 n 4-HYDROXYPROLINE HYDROXYPROLINE L-peptide linking H2 N 16.023 AMINO GROUP non-polymer C5 H9 N O2 115.130 y PROLINE L-peptide linking N 1 N C N 2 N O N 3 N C N 4 N H N 5 N H N 6 N H N 7 N H N 8 N N N 9 N C N 10 N C N 11 N O N 12 N C Y 13 N C Y 14 N C Y 15 N C Y 16 N C Y 17 N C Y 18 N C N 19 N N N 20 N O N 21 N O N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N O N 32 N H N 33 N N N 34 N C N 35 N C N 36 N O N 37 N O N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N O N 44 N H N 45 N H N 46 N N N 47 S C N 48 N C N 49 N O N 50 N C N 51 R C N 52 N C N 53 N O N 54 N O N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N N N 65 N H N 66 N H N 67 N N N 68 S C N 69 N C N 70 N O N 71 N C N 72 N C N 73 N C N 74 N O N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing Y 7 N doub Y 8 N sing Y 9 N sing N 10 N doub Y 11 N doub N 12 N sing Y 13 N doub N 14 N sing Y 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N doub N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N doub N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N doub N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing To Be Published 0353 Structure of collagen-like peptides with N-linked peptoid substitutions 10.2210/pdb9pug/pdb pdb_00009pug 100 1 N PIXEL 2021-05-20 DECTRIS PILATUS3 6M SINGLE WAVELENGTH M x-ray 1 0.97946 1.0 BL9-2 SSRL 0.97946 SYNCHROTRON SSRL BEAMLINE BL9-2 1992.087 N-nitrobenzyl Peptoid-modified Collagen 3 syn polymer 18.015 water 98 nat water no yes (ACE)GP(HYP)GP(HYP)GP(HYP)GP(EZY)GP(HYP)GP(HYP)GP(HYP)(NH2) XGPPGPPGPPGPXGPPGPPGPPX D,E,F polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n 1 1.74 29.43 VAPOR DIFFUSION, SITTING DROP protein at 10 mg/ml in water mixed 50:50 with 30% (w/v) PEG 8000, 200 mM Ammonium sulfate 277 repository Initial release 1 0 2026-04-08 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01AR071358 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) S10OD021527 michael.yu@utah.edu 0000-0002-5171-2644 Michael Yu S principal investigator/group leader N RCSB Y RCSB 2025-07-30 REL REL EZY EZY SUBJECT OF INVESTIGATION HOH water 9606 human Homo sapiens sample 1 23 Y Y D HYP 3 Named protein modification A HYP 4 PRO HYP 1 1_555 Hydroxylation D HYP 6 Named protein modification A HYP 7 PRO HYP 1 1_555 Hydroxylation D HYP 9 Named protein modification A HYP 10 PRO HYP 1 1_555 Hydroxylation D HYP 15 Named protein modification A HYP 16 PRO HYP 1 1_555 Hydroxylation D HYP 18 Named protein modification A HYP 19 PRO HYP 1 1_555 Hydroxylation D HYP 21 Named protein modification A HYP 22 PRO HYP 1 1_555 Hydroxylation E HYP 3 Named protein modification B HYP 4 PRO HYP 1 1_555 Hydroxylation E HYP 6 Named protein modification B HYP 7 PRO HYP 1 1_555 Hydroxylation E HYP 9 Named protein modification B HYP 10 PRO HYP 1 1_555 Hydroxylation E HYP 15 Named protein modification B HYP 16 PRO HYP 1 1_555 Hydroxylation E HYP 18 Named protein modification B HYP 19 PRO HYP 1 1_555 Hydroxylation E HYP 21 Named protein modification B HYP 22 PRO HYP 1 1_555 Hydroxylation F HYP 3 Named protein modification C HYP 4 PRO HYP 1 1_555 Hydroxylation F HYP 6 Named protein modification C HYP 7 PRO HYP 1 1_555 Hydroxylation F HYP 9 Named protein modification C HYP 10 PRO HYP 1 1_555 Hydroxylation F HYP 15 Named protein modification C HYP 16 PRO HYP 1 1_555 Hydroxylation F HYP 18 Named protein modification C HYP 19 PRO HYP 1 1_555 Hydroxylation F HYP 21 Named protein modification C HYP 22 PRO HYP 1 1_555 Hydroxylation D EZY 12 Non-standard residue A EZY 13 GLY EZY 1 1_555 None E EZY 12 Non-standard residue B EZY 13 GLY EZY 1 1_555 None F EZY 12 Non-standard residue C EZY 13 GLY EZY 1 1_555 None D ACE 0 Terminal acetylation A ACE 1 D GLY 1 GLY A GLY 2 1_555 ACE 12 1_555 None E ACE 0 Terminal acetylation B ACE 1 E GLY 1 GLY B GLY 2 1_555 ACE 12 1_555 None F ACE 0 Terminal acetylation C ACE 1 F GLY 1 GLY C GLY 2 1_555 ACE 12 1_555 None D NH2 22 Terminal amidation A NH2 23 D HYP 21 HYP A HYP 22 1_555 NH2 42 1_555 None E NH2 22 Terminal amidation B NH2 23 E HYP 21 HYP B HYP 22 1_555 NH2 42 1_555 None F NH2 22 Terminal amidation C NH2 23 F HYP 21 HYP C HYP 22 1_555 NH2 42 1_555 None HOH 101 2 HOH HOH 101 D HOH 102 2 HOH HOH 102 D HOH 103 2 HOH HOH 103 D HOH 104 2 HOH HOH 104 D HOH 105 2 HOH HOH 105 D HOH 106 2 HOH HOH 106 D HOH 107 2 HOH HOH 107 D HOH 108 2 HOH HOH 108 D HOH 109 2 HOH HOH 109 D HOH 110 2 HOH HOH 110 D HOH 111 2 HOH HOH 111 D HOH 112 2 HOH HOH 112 D HOH 113 2 HOH HOH 113 D HOH 114 2 HOH HOH 114 D HOH 115 2 HOH HOH 115 D HOH 116 2 HOH HOH 116 D HOH 117 2 HOH HOH 117 D HOH 118 2 HOH HOH 118 D HOH 119 2 HOH HOH 119 D HOH 120 2 HOH HOH 120 D HOH 121 2 HOH HOH 121 D HOH 122 2 HOH HOH 122 D HOH 123 2 HOH HOH 123 D HOH 124 2 HOH HOH 124 D HOH 125 2 HOH HOH 125 D HOH 126 2 HOH HOH 126 D HOH 127 2 HOH HOH 127 D HOH 128 2 HOH HOH 128 D HOH 129 2 HOH HOH 129 D HOH 130 2 HOH HOH 130 D HOH 101 2 HOH HOH 101 E HOH 102 2 HOH HOH 102 E HOH 103 2 HOH HOH 103 E HOH 104 2 HOH HOH 104 E HOH 105 2 HOH HOH 105 E HOH 106 2 HOH HOH 106 E HOH 107 2 HOH HOH 107 E HOH 108 2 HOH HOH 108 E HOH 109 2 HOH HOH 109 E HOH 110 2 HOH HOH 110 E HOH 111 2 HOH HOH 111 E HOH 112 2 HOH HOH 112 E HOH 113 2 HOH HOH 113 E HOH 114 2 HOH HOH 114 E HOH 115 2 HOH HOH 115 E HOH 116 2 HOH HOH 116 E HOH 117 2 HOH HOH 117 E HOH 118 2 HOH HOH 118 E HOH 119 2 HOH HOH 119 E HOH 120 2 HOH HOH 120 E HOH 121 2 HOH HOH 121 E HOH 122 2 HOH HOH 122 E HOH 123 2 HOH HOH 123 E HOH 124 2 HOH HOH 124 E HOH 125 2 HOH HOH 125 E HOH 126 2 HOH HOH 126 E HOH 127 2 HOH HOH 127 E HOH 128 2 HOH HOH 128 E HOH 129 2 HOH HOH 129 E HOH 130 2 HOH HOH 130 E HOH 131 2 HOH HOH 131 E HOH 101 2 HOH HOH 101 F HOH 102 2 HOH HOH 102 F HOH 103 2 HOH HOH 103 F HOH 104 2 HOH HOH 104 F HOH 105 2 HOH HOH 105 F HOH 106 2 HOH HOH 106 F HOH 107 2 HOH HOH 107 F HOH 108 2 HOH HOH 108 F HOH 109 2 HOH HOH 109 F HOH 110 2 HOH HOH 110 F HOH 111 2 HOH HOH 111 F HOH 112 2 HOH HOH 112 F HOH 113 2 HOH HOH 113 F HOH 114 2 HOH HOH 114 F HOH 115 2 HOH HOH 115 F HOH 116 2 HOH HOH 116 F HOH 117 2 HOH HOH 117 F HOH 118 2 HOH HOH 118 F HOH 119 2 HOH HOH 119 F HOH 120 2 HOH HOH 120 F HOH 121 2 HOH HOH 121 F HOH 122 2 HOH HOH 122 F HOH 123 2 HOH HOH 123 F HOH 124 2 HOH HOH 124 F HOH 125 2 HOH HOH 125 F HOH 126 2 HOH HOH 126 F HOH 127 2 HOH HOH 127 F HOH 128 2 HOH HOH 128 F HOH 129 2 HOH HOH 129 F HOH 130 2 HOH HOH 130 F HOH 131 2 HOH HOH 131 F HOH 132 2 HOH HOH 132 F HOH 133 2 HOH HOH 133 F HOH 134 2 HOH HOH 134 F HOH 135 2 HOH HOH 135 F HOH 136 2 HOH HOH 136 F HOH 137 2 HOH HOH 137 F ACE 0 n 1 ACE 0 D GLY 1 n 2 GLY 1 D PRO 2 n 3 PRO 2 D HYP 3 n 4 HYP 3 D GLY 4 n 5 GLY 4 D PRO 5 n 6 PRO 5 D HYP 6 n 7 HYP 6 D GLY 7 n 8 GLY 7 D PRO 8 n 9 PRO 8 D HYP 9 n 10 HYP 9 D GLY 10 n 11 GLY 10 D PRO 11 n 12 PRO 11 D EZY 12 n 13 EZY 12 D GLY 13 n 14 GLY 13 D PRO 14 n 15 PRO 14 D HYP 15 n 16 HYP 15 D GLY 16 n 17 GLY 16 D PRO 17 n 18 PRO 17 D HYP 18 n 19 HYP 18 D GLY 19 n 20 GLY 19 D PRO 20 n 21 PRO 20 D HYP 21 n 22 HYP 21 D NH2 22 n 23 NH2 22 D ACE 0 n 1 ACE 0 E GLY 1 n 2 GLY 1 E PRO 2 n 3 PRO 2 E HYP 3 n 4 HYP 3 E GLY 4 n 5 GLY 4 E PRO 5 n 6 PRO 5 E HYP 6 n 7 HYP 6 E GLY 7 n 8 GLY 7 E PRO 8 n 9 PRO 8 E HYP 9 n 10 HYP 9 E GLY 10 n 11 GLY 10 E PRO 11 n 12 PRO 11 E EZY 12 n 13 EZY 12 E GLY 13 n 14 GLY 13 E PRO 14 n 15 PRO 14 E HYP 15 n 16 HYP 15 E GLY 16 n 17 GLY 16 E PRO 17 n 18 PRO 17 E HYP 18 n 19 HYP 18 E GLY 19 n 20 GLY 19 E PRO 20 n 21 PRO 20 E HYP 21 n 22 HYP 21 E NH2 22 n 23 NH2 22 E ACE 0 n 1 ACE 0 F GLY 1 n 2 GLY 1 F PRO 2 n 3 PRO 2 F HYP 3 n 4 HYP 3 F GLY 4 n 5 GLY 4 F PRO 5 n 6 PRO 5 F HYP 6 n 7 HYP 6 F GLY 7 n 8 GLY 7 F PRO 8 n 9 PRO 8 F HYP 9 n 10 HYP 9 F GLY 10 n 11 GLY 10 F PRO 11 n 12 PRO 11 F EZY 12 n 13 EZY 12 F GLY 13 n 14 GLY 13 F PRO 14 n 15 PRO 14 F HYP 15 n 16 HYP 15 F GLY 16 n 17 GLY 16 F PRO 17 n 18 PRO 17 F HYP 18 n 19 HYP 18 F GLY 19 n 20 GLY 19 F PRO 20 n 21 PRO 20 F HYP 21 n 22 HYP 21 F NH2 22 n 23 NH2 22 F 0.0682 0.0538 -0.0248 0.0585 -0.0303 0.0259 -0.0011 0.0008 -0.0121 -0.0028 0.0073 -0.0001 -0.0049 -0.0002 0.0491 0.0840 -0.0028 0.0726 0.0446 0.0026 0.1669 refined 6.1796 -0.5670 -0.8614 X-RAY DIFFRACTION D 0 D 22 X-RAY DIFFRACTION 1 all E 0 E 22 X-RAY DIFFRACTION 1 all F 0 F 22 X-RAY DIFFRACTION 1 all S 1 S 98 X-RAY DIFFRACTION 1 all author_and_software_defined_assembly PISA 3 trimeric none 4460 -18 3890 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 D F O O HOH HOH 123 106 2.15 1_555 1_545 32.220 12.5154 7.770 0.2526 0.2156 0.2193 1.2980 31.6360 1018 9164 10182 10.0000 95.1700 0.1700 1 THROUGHOUT 1.330 MOLECULAR REPLACEMENT 30.0500 0.9000 1.1100 collagen peptide ML FLAT BULK SOLVENT MODEL 1.2980 31.6360 98 536 21.03 17.01 9 0 429 66 0.3601 0.0000 0.3092 1.3666 138 1246 91.0000 0.3060 0.0000 0.2899 1.4522 144 1263 95.0000 0.2936 0.0000 0.2720 1.5643 141 1297 95.0000 0.2744 0.0000 0.2446 1.7217 149 1337 97.0000 0.2623 0.0000 0.2317 1.9708 146 1282 94.0000 0.2472 0.0000 0.1941 2.4829 142 1337 97.0000 0.2070 0.0000 0.1767 31.6360 158 1402 96.0000 1.2980 31.640 9PUG 10264 0.998 0.209 0.042 0.213 1 11.500 25.300 96.100 2.485 1.300 1.320 10523 473 0.661 0.523 2.542 1 1.500 22.200 89.500 0.108 7.110 31.640 1729 80 0.999 0.022 0.110 1 28.400 21.600 98.200 data reduction XDS data scaling Aimless 0.7.4 refinement PHENIX 1.16_3549 data extraction PDB_EXTRACT 3.27 phasing PHASER N Crystal Structure of N-nitrobenzyl Peptoid-modified Collagen Triple Helix (GPX) 1 N N 1 N N 1 N N 2 N N 2 N N 2 N N covale 1.327 both D ACE 0 A C ACE 1 1_555 D GLY 1 A N GLY 2 1_555 covale 1.328 both D PRO 2 A C PRO 3 1_555 D HYP 3 A N HYP 4 1_555 covale 1.316 both D HYP 3 A C HYP 4 1_555 D GLY 4 A N GLY 5 1_555 covale 1.320 both D PRO 5 A C PRO 6 1_555 D HYP 6 A N HYP 7 1_555 covale 1.320 both D HYP 6 A C HYP 7 1_555 D GLY 7 A N GLY 8 1_555 covale 1.324 both D PRO 8 A C PRO 9 1_555 D HYP 9 A N HYP 10 1_555 covale 1.317 both D HYP 9 A C HYP 10 1_555 D GLY 10 A N GLY 11 1_555 covale 1.328 both D PRO 11 A C PRO 12 1_555 D EZY 12 A N EZY 13 1_555 covale 1.323 both D EZY 12 A C EZY 13 1_555 D GLY 13 A N GLY 14 1_555 covale 1.323 both D PRO 14 A C PRO 15 1_555 D HYP 15 A N HYP 16 1_555 covale 1.315 both D HYP 15 A C HYP 16 1_555 D GLY 16 A N GLY 17 1_555 covale 1.320 both D PRO 17 A C PRO 18 1_555 D HYP 18 A N HYP 19 1_555 covale 1.324 both D HYP 18 A C HYP 19 1_555 D GLY 19 A N GLY 20 1_555 covale 1.325 both D PRO 20 A C PRO 21 1_555 D HYP 21 A N HYP 22 1_555 covale 1.326 both D HYP 21 A C HYP 22 1_555 D NH2 22 A N NH2 23 1_555 covale 1.324 both E ACE 0 B C ACE 1 1_555 E GLY 1 B N GLY 2 1_555 covale 1.327 both E PRO 2 B C PRO 3 1_555 E HYP 3 B N HYP 4 1_555 covale 1.319 both E HYP 3 B C HYP 4 1_555 E GLY 4 B N GLY 5 1_555 covale 1.319 both E PRO 5 B C PRO 6 1_555 E HYP 6 B N HYP 7 1_555 covale 1.330 both E HYP 6 B C HYP 7 1_555 E GLY 7 B N GLY 8 1_555 covale 1.328 both E PRO 8 B C PRO 9 1_555 E HYP 9 B N HYP 10 1_555 covale 1.319 both E HYP 9 B C HYP 10 1_555 E GLY 10 B N GLY 11 1_555 covale 1.333 both E PRO 11 B C PRO 12 1_555 E EZY 12 B N EZY 13 1_555 covale 1.330 both E EZY 12 B C EZY 13 1_555 E GLY 13 B N GLY 14 1_555 covale 1.331 both E PRO 14 B C PRO 15 1_555 E HYP 15 B N HYP 16 1_555 covale 1.321 both E HYP 15 B C HYP 16 1_555 E GLY 16 B N GLY 17 1_555 covale 1.318 both E PRO 17 B C PRO 18 1_555 E HYP 18 B N HYP 19 1_555 covale 1.318 both E HYP 18 B C HYP 19 1_555 E GLY 19 B N GLY 20 1_555 covale 1.329 both E PRO 20 B C PRO 21 1_555 E HYP 21 B N HYP 22 1_555 covale 1.326 both E HYP 21 B C HYP 22 1_555 E NH2 22 B N NH2 23 1_555 covale 1.330 both F ACE 0 C C ACE 1 1_555 F GLY 1 C N GLY 2 1_555 covale 1.330 both F PRO 2 C C PRO 3 1_555 F HYP 3 C N HYP 4 1_555 covale 1.322 both F HYP 3 C C HYP 4 1_555 F GLY 4 C N GLY 5 1_555 covale 1.328 both F PRO 5 C C PRO 6 1_555 F HYP 6 C N HYP 7 1_555 covale 1.323 both F HYP 6 C C HYP 7 1_555 F GLY 7 C N GLY 8 1_555 covale 1.317 both F PRO 8 C C PRO 9 1_555 F HYP 9 C N HYP 10 1_555 covale 1.317 both F HYP 9 C C HYP 10 1_555 F GLY 10 C N GLY 11 1_555 covale 1.323 both F PRO 11 C C PRO 12 1_555 F EZY 12 C N EZY 13 1_555 covale 1.312 both F EZY 12 C C EZY 13 1_555 F GLY 13 C N GLY 14 1_555 covale 1.322 both F PRO 14 C C PRO 15 1_555 F HYP 15 C N HYP 16 1_555 covale 1.320 both F HYP 15 C C HYP 16 1_555 F GLY 16 C N GLY 17 1_555 covale 1.319 both F PRO 17 C C PRO 18 1_555 F HYP 18 C N HYP 19 1_555 covale 1.322 both F HYP 18 C C HYP 19 1_555 F GLY 19 C N GLY 20 1_555 covale 1.322 both F PRO 20 C C PRO 21 1_555 F HYP 21 C N HYP 22 1_555 covale 1.335 both F HYP 21 C C HYP 22 1_555 F NH2 22 C N NH2 23 1_555 STRUCTURAL PROTEIN N-linked nitrobenzyl, peptoid, NyBNZ, N-BNZ, collagen, STRUCTURAL PROTEIN 9PUG PDB 1 1 9PUG 0 22 9PUG 0 22 9PUG D 1 1 23 0 22 9PUG 0 22 9PUG E 1 1 23 0 22 9PUG 0 22 9PUG F 1 1 23 4 P 1 21 1