MolNFT v1 · #86854 · protein

Integrin ALPHA2 I domain E318W-collagen complex

4BJ3 · Integrin alpha-2: “Integrin ALPHA2 I domain E318W-collagen complex”. X-ray diffraction, 2 ligands (MG, CL), 4 pockets (best druggability 0.64). MolNFT v1 #86854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4BJ3
Type: protein
Length: 416 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrin alpha-2; Gfoger peptide
UniProt: P17301
Ligands: MG, CL
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrin alpha-2	protein	183	36% helix, 21% strand	P17301
B	Integrin alpha-2	protein	179	34% helix, 20% strand	P17301
C, D, E	Gfoger peptide	protein	18	0% helix, 0% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, E, B, C
CL · Chloride ion · ion · chains A
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B, C, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	548	0.64	0.76	41	empty
2	72	0.41	0.78	16	empty
3	81	0.39	0.78	15	empty
4	86	0.36	0.75	20	empty

Interfaces

10 interfaces between chains.

D–E · 590 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 580 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 527 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 345 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 328 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified (hydroxylation).

Compared structures

4BJ3 · Integrin alpha2 I domain E318W-collagen complex · the same entry in another collection · chain A against A, TM-score 1.00
P17301 · AlphaFold monomer V2.0 prediction for integrin alpha-2 (P17301) · a predicted model of the same protein · chain B against A, TM-score 0.94

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P17301
Elsewhere: RCSB PDB 4BJ3 · PDBe 4BJ3 · UniProt P17301

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