MolNFT v1 · #31682 · protein

VLA1 rdeltah I-domain complexed with a quadruple mutant of the AQC2 Fab

2B2X · Integrin alpha-1: “VLA1 rdeltah I-domain complexed with a quadruple mutant of the AQC2 Fab”. X-ray diffraction, 1 ligand (MG), 16 pockets (best druggability 0.70). MolNFT v1 #31682 on GenesisL1: 3D structure, binding sites and…

PDB: 2B2X
Type: protein
Length: 1,204 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrin alpha-1; Antibody AQC2 Fab
UniProt: P18614
Ligands: MG
Pockets: 16 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 21% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrin alpha-1	protein	188	38% helix, 21% strand	P18614
H, I	Antibody AQC2 Fab	protein	210	6% helix, 55% strand	—
L, M	Antibody AQC2 Fab	protein	210	6% helix, 50% strand	—
B	Integrin alpha-1	protein	176	39% helix, 20% strand	P18614

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, H, B, I

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

Pockets

16 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	876	0.70	0.75	100	empty
2	165	0.62	0.84	28	empty
3	112	0.56	0.84	23	empty
4	172	0.56	0.80	26	empty
5	312	0.55	0.75	38	empty

Interfaces

8 interfaces between chains.

I–M · 1717 Å² buried · 13 hydrogen bonds · protein-protein
H–L · 1685 Å² buried · 13 hydrogen bonds · protein-protein
A–H · 631 Å² buried · 12 hydrogen bonds · protein-protein
B–I · 582 Å² buried · 12 hydrogen bonds · protein-protein
A–L · 474 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2B2X · VLA1 RdeltaH I-domain complexed with a quadruple mutant of the AQC2 Fab · the same entry in another collection · chain M against M, TM-score 1.00
P18614 · AlphaFold monomer V2.0 prediction for integrin alpha-1 (P18614) · a predicted model of the same protein · chain A 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 P18614
Elsewhere: RCSB PDB 2B2X · PDBe 2B2X · UniProt P18614

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