7Y37 | pdb_00007y37

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.183 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

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

Zhu, Y., Yang, X., Sun, F.

To be published.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

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

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Zhu, Y., Yang, X., Sun, F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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