SMTL ID : 8gce.1

The Extracellular Domain of Integrin AlphaIIbBeta3 in Intermediate State

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 1 residues within 4Å: Chain B: N.397 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 3 residues within 4Å: Chain A: R.312 Chain B: N.342, N.346 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.312

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 5 residues within 4Å: Chain B: P.47, D.122, K.124, N.125, E.426 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.47

6 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: E.274 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.274, A:E.274 CA.5: 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.6: 5 residues within 4Å: Chain A: D.396, D.398, D.400, Y.402, D.404 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.398, A:D.398, A:D.400, A:D.404, A:D.404 CA.7: 5 residues within 4Å: Chain A: D.457, D.459, N.461, Y.463, D.465 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.457, A:D.459, A:D.465, A:D.465 CA.11: 4 residues within 4Å: Chain B: S.149, D.152, D.153, D.277 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.149, B:D.277 CA.12: 6 residues within 4Å: Chain B: D.184, N.241, D.243, P.245, E.246, H.281 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.184, B:D.243, B:P.245

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.8: 1 residues within 4Å: Chain A: N.46 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: E.538, R.543, N.601, H.622 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.538, A:N.601 Hydrogen bonds: A:E.538, A:R.543, A:N.601

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain B: S.147, S.149, A.244, E.246, A.278 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.147, B:E.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huo, T. et al., Full-length alpha IIb beta 3 cryo-EM structure reveals intact integrin initiate-activation intrinsic architecture. Structure (2024)

Release Date

2024-03-06

Peptides

Integrin alpha-IIb: A
Integrin beta-3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-IIb

Integrin beta-3