6Q41 | pdb_00006q41

Atomic resolution crystal structure of a BAA collagen heterotrimer

• PDB DOI: https://doi.org/10.2210/pdb6Q41/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: 1.03 Å
• R-Value Free: 
  0.177 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

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

Local Symmetry: Helical - H  (Explore in 3D)
Local 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: 13.79 kDa 
• Atom Count: 1,305 
• Modeled Residue Count: 150 
• Deposited Residue Count: 150 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Middle and Trailing Chains of the BAA collagen heterotrimer	A [auth B], B [auth C]	50	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leading chain of the BAA collagen heterotrimer	C [auth A]	50	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth C], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth B], E [auth B], F [auth B], G [auth B], H [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free:  0.177 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 18.777	α = 69.039
b = 38.656	β = 79.584
c = 45.329	γ = 77.438

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	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