SMTL ID : 9e8c.1

Integrin aIIbb3 dimer conformation from human platelet membrane crude preparation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-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: 7 residues within 4Å: Chain A: W.293, L.295, R.312, M.316 Chain B: N.342, L.343, N.346 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.312, A:R.312 NAG-NAG-BMA.4: 4 residues within 4Å: Chain C: R.312, M.316 Chain D: L.343, N.346 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.312, C:R.312

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.2: 3 residues within 4Å: Chain D: K.124, N.125 Ligands: NAG.27 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.125 NAG-NAG.5: 7 residues within 4Å: Chain D: N.475, N.476, N.478, W.492, E.498, S.500, Q.509 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:E.498, D:Q.509 Hydrogen bonds: D:S.500, D:S.500, D:S.500, D:Q.509, D:Q.509

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: 3 residues within 4Å: Chain B: N.475, N.476, W.492 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.492 Hydrogen bonds: B:N.475, B:N.475

12 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.332, R.334, D.336, L.363, Q.364 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.332, A:D.336, A:Q.364 CA.7: 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.276, A:T.281, A:T.281, A:E.283 CA.8: 8 residues within 4Å: Chain A: G.395, D.396, L.397, D.398, R.399, D.400, Y.402, D.404 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.396, A:D.398, A:D.400, A:D.404 CA.9: 6 residues within 4Å: Chain A: D.457, I.458, 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:Y.463, A:D.465 CA.14: 7 residues within 4Å: Chain B: D.184, N.241, D.243, A.244, P.245, E.246, H.281 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.243, B:D.243, B:D.243, B:P.245 CA.15: 5 residues within 4Å: Chain B: S.149, M.150, D.152, D.153, M.361 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.149, B:D.153 CA.17: 5 residues within 4Å: Chain C: D.328, N.330, D.332, R.334, D.336 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.328, C:D.332, C:R.334, C:D.336, C:D.336 CA.18: 5 residues within 4Å: Chain C: E.274, D.276, D.278, T.281, E.283 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.274, C:D.278, C:T.281, C:E.283, C:E.283 CA.19: 6 residues within 4Å: Chain C: D.396, D.398, D.400, Y.402, D.404, G.425 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.398, C:D.398, C:D.400, C:Y.402, C:D.404 CA.20: 5 residues within 4Å: Chain C: D.457, D.459, N.461, Y.463, D.465 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.457, C:D.459, C:Y.463, C:D.465 CA.25: 4 residues within 4Å: Chain D: D.184, K.185, Y.190, M.213 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.184, D:K.185 CA.26: 4 residues within 4Å: Chain D: S.149, D.152, D.153, M.361 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:S.149, D:D.152, D:D.152, D:D.153, D:M.361

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

NAG.10: 2 residues within 4Å: Chain A: L.279, N.280 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.280 Hydrogen bonds: A:N.280 NAG.11: 4 residues within 4Å: Chain A: E.538, N.601, S.603, H.622 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.601, A:S.603, A:H.622 NAG.12: 2 residues within 4Å: Chain A: N.46, N.474 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.46, A:N.474 NAG.16: 2 residues within 4Å: Chain B: K.124, N.125 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.124, B:N.125 NAG.21: 2 residues within 4Å: Chain C: D.278, N.280 No protein-ligand interaction detected (PLIP) NAG.22: 5 residues within 4Å: Chain C: E.538, S.599, N.601, S.603, H.622 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.538, C:S.599, C:N.601, C:S.603, C:S.603 NAG.23: 2 residues within 4Å: Chain C: N.46, G.47 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.46, C:G.47 NAG.27: 7 residues within 4Å: Chain D: S.395, F.396, N.397, S.424, I.425, E.426 Ligands: NAG-NAG.2 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.397, D:N.397, D:E.426

2 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 5 residues within 4Å: Chain B: D.145, S.147, S.149, E.246, D.277 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.147, B:D.277, B:D.277 MG.24: 5 residues within 4Å: Chain D: D.145, S.147, S.149, E.246, D.277 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.147, D:E.246

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: AC
Integrin beta-3: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Integrin alpha-IIb

Integrin beta-3

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