MolNFT v1 · #144557 · protein

Crystal structure of an extended B3 integrin P33

6BXB · Chimera protein of integrin beta-3 and integrin alpha-L: “Crystal structure of an extended B3 integrin P33”. X-ray diffraction, 3 ligands (NAG, CA, MG), 7 pockets (best druggability 0.64). MolNFT v1 #144557 on GenesisL1: 3D…

PDB: 6BXB
Type: protein
Length: 928 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chimera protein of integrin beta-3 and integrin alpha-L
UniProt: P05106, P20701
Ligands: NAG, CA, MG
Pockets: 7 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chimera protein of integrin beta-3 and integrin alpha-L	protein	463	21% helix, 30% strand	P05106, P20701
B	Chimera protein of integrin beta-3 and integrin alpha-L	protein	465	18% helix, 29% strand	P05106, P20701

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
CA · Calcium ion · metal · chains A
MG · Magnesium ion · metal · chains B
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	289	0.64	0.81	34	empty
2	256	0.64	0.82	36	empty
3	365	0.56	0.74	40	empty
4	319	0.56	0.76	32	empty
5	169	0.48	0.77	27	empty

Interfaces

1 interface between chains.

A–B · 270 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 26 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

6BXB · Crystal structure of an extended b3 integrin P33 · the same entry in another collection · chain A against A, TM-score 1.00
P20701 · AlphaFold monomer V2.0 prediction for integrin alpha-L (P20701) · a predicted model of the same protein · chain A against A, TM-score 0.43

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 P05106
Every structure of UniProt P20701
Elsewhere: RCSB PDB 6BXB · PDBe 6BXB · UniProt P05106 · UniProt P20701

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