9PUF | pdb_00009puf

Crystal Structure of N-Phenylalanine Peptoid-modified Collagen Triple Helix (GPX)

PDB DOI: https://doi.org/10.2210/pdb9PUF/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2025-07-30 Released: 2026-04-08
Deposition Author(s): Whitby, F.G., Ratnitilakanabhuket, P.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.168 (Depositor), 0.173 (DCC)
R-Value Work:
0.147 (Depositor), 0.154 (DCC)
R-Value Observed:
0.149 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of collagen-like peptides with N-linked peptoid substitutions

Whitby, F.G., Ratnatilakanabhuket, P.

To be published.

Macromolecule Content

Total Structure Weight: 5.84 kDa
Atom Count: 515
Modeled Residue Count: 67
Deposited Residue Count: 69
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-Phenylalanine Peptoid-modified Collagen	A [auth D], B [auth E], C [auth F]	23	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP Query on HYP	A [auth D], B [auth E], C [auth F]	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.168 (Depositor), 0.173 (DCC)
R-Value Work: 0.147 (Depositor), 0.154 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.541	α = 90
b = 24.081	β = 94.5
c = 15.029	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-04-08

Deposition Author(s):

Ratnitilakanabhuket, P.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01AR071358
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10OD021527

Revision History (Full details and data files)

Version 1.0: 2026-04-08
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.