SMTL ID : 7tpd.2 (1 other biounit)

Integrin alaphIIBbeta3 complex with EF5154

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-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.1: 5 residues within 4Å: Chain A: R.281, M.285 Chain B: N.316, L.317, N.320 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.281

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.2: 6 residues within 4Å: Chain B: S.369, N.371, S.398, I.399, E.400 Ligands: NAG.12 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 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:E.252 CA.4: 5 residues within 4Å: Chain A: D.297, N.299, D.301, R.303, D.305 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.297, A:D.301, A:R.303, A:D.305, H2O.1 CA.5: 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.367, A:D.369, A:Y.371, A:D.373, A:D.373 CA.6: 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.10: 4 residues within 4Å: Chain B: S.123, D.126, D.127, M.335 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:D.127, B:M.335, H2O.10, H2O.14 CA.11: 5 residues within 4Å: Chain B: D.158, N.215, D.217, P.219, E.220 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

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain A: A.89, R.90, H.112 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.112 Salt bridges: A:H.112, A:K.124 SO4.8: 4 residues within 4Å: Chain A: N.227, Y.230, R.276, R.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.227, A:R.279 Salt bridges: A:R.276

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain B: S.121, S.123, E.220 Ligands: IR7.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.121, B:S.123, B:E.220, H2O.10, H2O.11

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

NAG.12: 4 residues within 4Å: Chain B: N.99, F.100, S.101 Ligands: NAG-NAG.2 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.98, B:N.99 Water bridges: B:K.98, B:K.98, B:K.98

1 x IR7: (4-{[2-oxo-4-(piperidin-4-yl)piperazin-1-yl]acetyl}phenoxy)acetic acid(Non-covalent)

IR7.13: 18 residues within 4Å: Chain A: D.159, F.160, Y.189, Y.190, L.192, D.224, S.225, F.231 Chain B: S.121, Y.122, S.123, R.214, N.215, R.216, D.217, A.218, E.220 Ligands: MG.9 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.218, A:F.160, A:Y.190, A:L.192, A:F.231 Hydrogen bonds: B:Y.122, B:S.123, B:N.215, B:N.215, A:Y.189 Water bridges: B:S.121, B:S.123, B:S.123, A:W.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, J. et al., Integrin alpha IIB beta 3 headpiece with Fab complex with EF5154. To Be Published

Release Date

2022-08-17

Peptides

Integrin alpha-IIb heavy chain: A
Integrin beta-3: B
Fab heavy chain: C
Fab light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

Integrin alpha-IIb heavy chain

Integrin beta-3

Fab heavy chain

Fab light chain

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