8YV3 | pdb_00008yv3

The heterotrimer structure of peptides derived from human collagen type I

• PDB DOI: https://doi.org/10.2210/pdb8YV3/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-03-27 Released: 2025-04-02 
• 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: 1.68 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

The heterotrimer structure of peptides derived from human collagen type I

Zhu, Y., Yang, X., Sun, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Helical - H  (Explore in 3D)
Pseudo Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.64 kDa 
• Atom Count: 1,564 
• Modeled Residue Count: 184 
• Deposited Residue Count: 186 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-1(I) chain	A, D	31	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P02452 (Homo sapiens) Explore P02452  Go to UniProtKB:  P02452
PHAROS:  P02452 GTEx:  ENSG00000108821

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-2(I) chain	B, C, E, F	31	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P08123 (Homo sapiens) Explore P08123  Go to UniProtKB:  P08123
PHAROS:  P08123 GTEx:  ENSG00000164692

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.49	α = 82.17
b = 33.043	β = 77.73
c = 38.519	γ = 69.64

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
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: 2025-04-02
  Type: Initial release