6Q43

Atomic resolution crystal structure of an ABA collagen heterotrimer

• PDB DOI: https://doi.org/10.2210/pdb6Q43/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2018-12-05 Released: 2019-12-18 
• Deposition Author(s): Jalan, A.A., Hartgerink, J.D., Brear, P., Leitinger, B., Farndale, R.W.
• Funding Organization(s): Royal Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 0.177 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 

Starting Model: experimental

Literature

Atomic resolution crystal structure of an AAB collagen heterotrimer

Jalan, A.A., Hartgerink, J.D., Brear, P., Leitinger, B., Farndale, R.W.

(2019) Nat Chem Biol 

• DOI: https://doi.org/10.1038/s41589-019-0435-y

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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 12.74 kDa 
• Atom Count: 1,169 
• Modelled Residue Count: 139 
• Deposited Residue Count: 139 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leading Chain of the ABA collagen heterotrimer	A	46	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Middle Chain of the ABA collagen heterotrimer	B	47	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Trailing chain of the ABA collagen heterotrimer	C	46	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	A	L-PEPTIDE LINKING	C5 H9 N O3		PRO
NLE	A	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 0.177 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.339	α = 90
b = 26.652	β = 92.24
c = 64.457	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Jalan, A.A., Hartgerink, J.D., Brear, P., Leitinger, B., Farndale, R.W.

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Funding Organization	Location	Grant Number
Royal Society	United Kingdom	NF140721

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description