SMTL ID : 9e8a.1

Integrin aIIbb3 bent conformation from human platelet membrane crude preparation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x GLY- ARG- GLY- ASP: GLY-ARG-GLY-ASP(Non-covalent)

GLY-ARG-GLY-ASP.1: 17 residues within 4Å: Chain A: D.190, F.191, Y.220, Y.221, L.223, D.255, F.262 Chain B: S.147, Y.148, S.149, R.240, N.241, R.242, D.243, A.244, E.246 Ligands: MG.17 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.221 Hydrogen bonds: A:F.191, A:Y.220, B:Y.148, B:S.149, B:N.241, B:N.241, B:N.241, B:R.242 Salt bridges: A:D.255

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

NAG-NAG.2: 3 residues within 4Å: Chain A: N.601, S.603, H.622 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.125, F.126, S.127 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: V.661, M.691, R.692 Chain B: Y.557, Y.583, N.585, C.609 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: W.960, N.962, R.977 No protein-ligand interaction detected (PLIP)

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.6: 6 residues within 4Å: Chain B: S.395, N.397, P.407, S.424, I.425, E.426 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 2 residues within 4Å: Chain A: R.312 Chain B: N.346 No protein-ligand interaction detected (PLIP)

1 x BMA- BMA- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose

BMA-BMA-NAG-NAG.8: 4 residues within 4Å: Chain B: N.475, N.476, N.478, W.492 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.492 Hydrogen bonds: B:N.475, B:N.476, B:N.478

7 x CA: CALCIUM ION(Non-covalent)

CA.9: 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.10: 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.11: 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.396, A:D.398, A:D.400, A:Y.402, A:D.404 CA.12: 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.15: 5 residues within 4Å: Chain A: C.633, D.636, V.638, V.640, E.673 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.636, A:D.636, A:V.638, A:E.673, A:E.673 CA.18: 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:D.243, B:P.245 CA.19: 4 residues within 4Å: Chain B: S.149, D.152, D.153, M.361 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.149, B:D.152, B:D.152, B:D.153, B:M.361

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

NAG.13: 2 residues within 4Å: Chain A: D.278, N.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.278 NAG.14: 1 residues within 4Å: Chain A: N.46 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.46 NAG.16: 2 residues within 4Å: Chain A: N.711, E.712 No protein-ligand interaction detected (PLIP) NAG.20: 8 residues within 4Å: Chain A: G.808 Chain B: L.671, K.672, D.673, T.674, A.678, N.680, Q.694 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.671 Hydrogen bonds: B:L.671, B:D.673, B:D.673

1 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 5 residues within 4Å: Chain B: S.147, S.149, E.246, A.278 Ligands: GLY-ARG-GLY-ASP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B: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: A
Integrin beta-3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-IIb

Integrin beta-3

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