MolNFT v1 · #145315 · protein

Crystal structure of an extended BETA3 integrin P33

6CKB · Chimera protein of integrin beta-3 and integrin alpha-L: “Crystal structure of an extended BETA3 integrin P33”. X-ray diffraction, 3 ligands (NAG, MG, CA), 4 pockets (best druggability 0.80). MolNFT v1 #145315 on GenesisL1: 3D…

PDB: 6CKB
Type: protein
Length: 929 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, MG, CA
Pockets: 4 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chimera protein of integrin beta-3 and integrin alpha-L	protein	464	19% helix, 27% strand	P05106, P20701
B	Chimera protein of integrin beta-3 and integrin alpha-L	protein	465	16% helix, 26% strand	P05106, P20701

Ligands and binding sites

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

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	462	0.80	0.87	59	empty
2	319	0.66	0.81	45	empty
3	410	0.58	0.75	39	empty
4	201	0.47	0.74	31	empty

Modifications

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

Compared structures

6CKB · Crystal structure of an extended beta3 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 6CKB · PDBe 6CKB · UniProt P05106 · UniProt P20701

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