SMTL ID : 8t2u.1

Cryo-EM Structures of Full-length Integrin alphaIIbbeta3 in Native Lipids complexed with Eptifibatide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MPT- HRG- GLY- ASP- TRP- PRO- CYS- NH2: Eptifibatide(Non-covalent)

MPT-HRG-GLY-ASP-TRP-PRO-CYS-NH2.1: 18 residues within 4Å: Chain A: F.160, Y.189, Y.190, L.192, D.224, S.225, F.231, D.232 Chain B: S.121, Y.122, S.123, D.126, M.180, N.215, R.216, A.218, E.220 Ligands: MG.10 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.123, B:N.215, B:N.215, B:R.216, B:A.218, B:E.220 Water bridges: B:S.123, B:A.218 pi-Stacking: B:Y.122 Hydrophobic interactions: A:Y.190 Salt bridges: A:D.224

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.2: 1 residues within 4Å: Chain A: N.15 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.3: 2 residues within 4Å: Chain B: N.316, N.320 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.4: 6 residues within 4Å: Chain B: N.99, F.370, N.371, P.381, S.398 Ligands: NAG.13 No protein-ligand interaction detected (PLIP)

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

NAG.5: 1 residues within 4Å: Chain A: N.249 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain B: N.99 Ligands: NAG-NAG.4, NAG-NAG.4 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.245, D.247, T.250, T.251, E.252 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.245, A:D.247, A:T.250, A:T.250, A:E.252 CA.7: 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.8: 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.9: 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.11: 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 CA.12: 5 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, D.251 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.123, B:D.126, B:D.127, B:D.251, B:D.251

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain B: S.121, S.123, M.124, E.220 Ligands: MPT-HRG-GLY-ASP-TRP-PRO-CYS-NH2.1 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adair, B.D. et al., Cryo-EM structures of full-length integrin alpha IIb beta 3 in native lipids. Nat Commun (2023)

Release Date

2023-07-26

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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