MolNFT v1 · #121031 · protein

Integrin ALPHA2BETA1 I-domain

5HJ2 · Integrin alpha-2: “Integrin ALPHA2BETA1 I-domain”. X-ray diffraction, 3 ligands (CA, CL, SO4), 9 pockets (best druggability 0.80). MolNFT v1 #121031 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HJ2
Type: protein
Length: 1,177 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrin alpha-2
UniProt: P17301
Ligands: CA, CL, SO4
Pockets: 9 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	Integrin alpha-2	protein	197	40% helix, 21% strand	P17301
A, B, E	Integrin alpha-2	protein	196	39% helix, 21% strand	P17301
F	Integrin alpha-2	protein	195	38% helix, 21% strand	P17301

Ligands and binding sites

CA · Calcium ion · metal · 5 copies · chains C, A, B, D, E
CL · Chloride ion · ion · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
GOL · Glycerol · additive · 2 copies · chains F
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	929	0.80	0.82	110	SO4
2	210	0.65	0.84	34	empty
3	106	0.63	0.89	33	empty
4	172	0.62	0.84	40	empty
5	149	0.54	0.81	34	empty

Interfaces

8 interfaces between chains.

B–D · 721 Å² buried · 7 hydrogen bonds · protein-protein
C–A · 691 Å² buried · 6 hydrogen bonds · protein-protein
C–B · 479 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 383 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 367 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5HJ2 · Integrin alpha2beta1 I-domain · the same entry in another collection · chain F against F, TM-score 1.00
P17301 · AlphaFold monomer V2.0 prediction for integrin alpha-2 (P17301) · a predicted model of the same protein · chain F against A, TM-score 0.99

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 5HJ2 · PDBe 5HJ2 · UniProt P17301

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