SMTL ID : 9deq.1

Cryo-EM structures of full-length integrin alphaIIbbeta3 in native lipids complexed with modified tirofiban

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

3 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: 6 residues within 4Å: Chain A: G.796, H.798, W.929, N.931, V.932, S.933 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 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) NAG-NAG-BMA.6: 4 residues within 4Å: Chain B: N.449, N.450, N.452, W.466 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 3 residues within 4Å: Chain B: Y.531, Y.557, N.559 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: S.97, K.98, N.99, E.400 Ligands: NAG-NAG-BMA-BMA-BMA.4 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA.4: 7 residues within 4Å: Chain B: N.99, N.371, P.381, G.382, S.398, E.400 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP)

7 x CA: CALCIUM ION(Non-covalent)

CA.7: 7 residues within 4Å: Chain A: D.297, N.299, D.301, R.303, D.305, L.332, Q.333 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.301, A:R.303, A:D.305, A:D.305 CA.8: 6 residues within 4Å: Chain A: E.243, D.245, D.247, T.250, T.251, 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:T.250 CA.9: 8 residues within 4Å: Chain A: D.365, L.366, D.367, D.369, Y.371, D.373, L.393, G.394 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.367, A:D.369, A:Y.371, A:D.373, A:D.373 CA.10: 7 residues within 4Å: Chain A: D.426, D.428, N.430, Y.432, P.433, D.434, A.450 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.428, A:D.428, A:Y.432, A:D.434, A:D.434 CA.15: 7 residues within 4Å: Chain A: C.602, G.603, D.605, V.607, C.608, V.609, E.642 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.602, A:D.605, A:D.605, A:V.607, A:E.642 CA.18: 6 residues within 4Å: Chain B: D.158, N.215, D.217, A.218, P.219, E.220 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.158, B:D.217, B:D.217, B:E.220, B:E.220 CA.19: 5 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, M.335 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.123, B:D.126, B:D.127, H2O.1, H2O.1

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

NAG.11: 3 residues within 4Å: Chain A: D.247, L.248, N.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.248 NAG.12: 2 residues within 4Å: Chain A: E.679, N.680 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.679 NAG.13: 3 residues within 4Å: Chain A: N.570, S.572, H.591 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.570 NAG.14: 1 residues within 4Å: Chain A: N.15 No protein-ligand interaction detected (PLIP) NAG.16: 6 residues within 4Å: Chain B: K.646, G.649, A.652, V.653, N.654, Q.668 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.652 Hydrogen bonds: B:N.654

1 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 6 residues within 4Å: Chain B: S.121, N.215, A.218, E.220, A.252 Ligands: 01.20 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.121, B:E.220, H2O.1, H2O.1, H2O.1

1 x 01: N-(1,3-benzoxazole-2-carbonyl)-O-[4-(piperidin-4-yl)butyl]-L-tyrosine

01.20: 22 residues within 4Å: Chain A: D.159, F.160, S.161, W.162, D.163, Y.189, Y.190, L.192, D.224, S.225, S.226, F.231 Chain B: S.121, Y.122, S.123, R.214, N.215, R.216, D.217, A.218, E.220 Ligands: MG.17 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.190, B:A.218 Hydrogen bonds: A:D.224, B:S.121, B:N.215, B:N.215, B:N.215

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.21: 5 residues within 4Å: Chain B: I.707, A.710, A.711, I.714, L.718 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.707, B:I.714 CLR.22: 4 residues within 4Å: Chain B: L.694, L.697, M.701, L.705 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adair, B.D. et al., Platelet integrin alpha IIb beta 3 plays a key role in a venous thrombogenesis mouse model. Nat Commun (2024)

Release Date

2024-10-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Integrin alpha-IIb

Integrin beta-3

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