6Q3P | pdb_00006q3p

Atomic resolution crystal structure of an AAB collagen heterotrimer

• PDB DOI: https://doi.org/10.2210/pdb6Q3P/pdb

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


• Deposited: 2018-12-04 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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: in silico

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: Helical - H  (Explore in 3D)
Global 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: 13.42 kDa 
• Atom Count: 1,246 
• Modeled Residue Count: 148 
• Deposited Residue Count: 148 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leading Chain of the AAB Collagen Heterotrimer	A	49	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Middle Chain of the AAB Collagen Heterotrimer	B	50	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Trailing Chain of the AAB Collagen Heterotrimer	C	49	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.03 Å
• R-Value Free:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 19.736	α = 86.361
b = 28.076	β = 86.681
c = 48.384	γ = 77.21

Software Package:

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

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.

---

Funding Organization	Location	Grant Number
Royal Society	United Kingdom	NF140721

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description