SMTL ID : 9e8b.1

Integrin aIIbb3 intermediate conformation from human platelet membrane crude preparation

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: 5 residues within 4Å: Chain B: S.369, N.371, S.398, I.399, E.400 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: W.262, R.281, M.285 Chain B: N.316, L.317, N.320 No protein-ligand interaction detected (PLIP)

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

BMA-NAG-NAG.3: 6 residues within 4Å: Chain B: N.449, E.472, C.473, S.474, Q.482, Q.483 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.472, B:S.474, B:Q.483, B:Q.483

6 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.297, N.299, D.301, R.303, D.305 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.297, A:D.301, A:R.303, A:D.305, A:D.305 CA.5: 5 residues within 4Å: Chain A: E.243, D.245, D.247, T.250, E.252 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.243, A:D.245, A:D.247, A:T.250, A:E.252 CA.6: 5 residues within 4Å: Chain A: D.365, D.367, D.369, Y.371, D.373 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.365, A:D.367, A:D.369, A:Y.371, A:D.373 CA.7: 5 residues within 4Å: Chain A: D.426, D.428, N.430, Y.432, D.434 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.426, A:D.428, A:Y.432, A:D.434, A:D.434 CA.12: 5 residues within 4Å: Chain B: D.158, N.215, D.217, P.219, H.255 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.158, B:D.217, B:P.219 CA.13: 5 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, M.335 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.123, B:D.126, B:D.127, B:M.335

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

NAG.8: 1 residues within 4Å: Chain A: N.249 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: R.512, N.570, S.572, H.591 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.570 NAG.10: 1 residues within 4Å: Chain A: N.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.15 NAG.14: 3 residues within 4Å: Chain B: K.98, N.99, F.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.98, B:K.98

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 4 residues within 4Å: Chain B: S.121, S.123, E.220, D.251 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.121, B:S.123, B:E.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, X. et al., Elucidating the dynamics of integrin alpha IIb beta 3 from native platelet membranes by cryo-EM with build-and-retrieve method. Blood Adv (2025)

Release Date

2025-10-15

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