SMTL ID : 9der.1

Cryo-EM Structures of Full-Length Integrin alphaIIbbeta3 in Native Lipids Complexed with Tirofiban

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 A: N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 6 residues within 4Å: Chain B: N.99, N.371, V.379, P.381, S.398 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA: 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.2: 7 residues within 4Å: Chain A: L.264, R.281, E.283, Q.284, M.285 Chain B: N.316, N.320 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-4)-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.3: 2 residues within 4Å: Chain A: N.15, G.16 No protein-ligand interaction detected (PLIP)

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.5: 5 residues within 4Å: Chain B: K.98, N.99, F.100, S.101 Ligands: NAG-NAG-BMA.4 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: D.245, D.247, T.250, E.252 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.245, A:D.245, A:D.247, A:T.250, A:E.252 CA.7: 7 residues within 4Å: Chain A: D.297, N.299, D.301, R.303, H.304, D.305, Q.333 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:R.303, A:D.305 CA.8: 7 residues within 4Å: Chain A: D.365, L.366, D.367, D.369, Y.371, D.373, L.393 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.365, A:D.367, A:Y.371, A:D.373 CA.9: 6 residues within 4Å: Chain A: D.426, I.427, 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.11: 5 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, D.251 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.123, B:D.126, B:D.126, B:D.251 CA.12: 6 residues within 4Å: Chain B: D.158, N.215, D.217, P.219, E.220, H.255 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.158, B:D.217, B:D.217, B:P.219, B:E.220

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 7 residues within 4Å: Chain B: S.121, S.123, M.124, N.215, A.218, E.220 Ligands: AGG.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.121, B:S.123, B:E.220, H2O.1, H2O.1

1 x AGG: TIROFIBAN(Non-covalent)

AGG.13: 24 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, D.232 Chain B: S.121, Y.122, S.123, Y.166, R.214, N.215, R.216, D.217, A.218, E.220 Ligands: MG.10 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.218, A:F.160, A:F.160, A:Y.190, A:Y.190, A:F.231 Hydrogen bonds: B:Y.122, B:S.123, B:S.123, B:Y.166, B:R.214, B:R.214, B:N.215, B:N.215, B:R.216, A:D.224 Water bridges: B:S.123

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

Integrin alpha-IIb

Integrin beta-3

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