7Y37

Structure of a triple-helix region of human collagen type V

PDB DOI: https://doi.org/10.2210/pdb7Y37/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: synthetic construct
Mutation(s): No

Deposited: 2022-06-10 Released: 2023-07-05
Deposition Author(s): Zhu, Y., Yang, X., Sun, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.183
R-Value Work: 0.156
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of a triple-helix region of human collagen type V

Zhu, Y., Yang, X., Sun, F.

To be published.

Macromolecule Content

Total Structure Weight: 7.59 kDa
Atom Count: 735
Modelled Residue Count: 87
Deposited Residue Count: 87
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A triple-helix region of human collagen type V	A, B, C	29	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P20908 (Homo sapiens) Explore P20908 Go to UniProtKB: P20908
PHAROS: P20908 GTEx: ENSG00000130635
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20908
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.183
R-Value Work: 0.156
R-Value Observed: 0.157
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.865	α = 90
b = 23.675	β = 100.19
c = 36.648	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.