SMTL ID : 9axl.1

Structure of the semi-extended AlphaIIbBeta3 in complex with R21D10 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.274, D.276, D.278, T.281, T.282, E.283 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.274, A:D.278, A:T.281, A:T.281, A:E.283 CA.2: 5 residues within 4Å: Chain A: D.328, N.330, D.332, R.334, D.336 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.328, A:D.332, A:R.334, A:D.336, A:D.336 CA.3: 5 residues within 4Å: Chain A: D.396, D.398, D.400, Y.402, D.404 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.400, A:Y.402, A:D.404, A:D.404 CA.4: 5 residues within 4Å: Chain A: D.457, D.459, N.461, Y.463, D.465 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.457, A:D.459, A:Y.463, A:D.465, A:D.465 CA.5: 4 residues within 4Å: Chain B: S.149, D.152, D.153, M.361 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.152, B:D.152, H2O.1 CA.6: 5 residues within 4Å: Chain B: D.184, N.241, D.243, P.245, E.246 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.184, B:D.243, B:P.245, B:E.246

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain B: S.147, A.244, E.246, A.278 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.246, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., An alpha IIb beta 3 monoclonal antibody traps a semiextended conformation and allosterically inhibits large ligand binding. Blood Adv (2024)

Release Date

2024-11-13

Peptides

Integrin alpha-IIb: A
Integrin beta-3: B
R21D10 Fab heavy chain: C
R21D10 Fab light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Integrin alpha-IIb

Integrin beta-3

R21D10 Fab heavy chain

R21D10 Fab light chain

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