SMTL ID : 7l8p.1 (2 other biounits)

Integrin alphaIIbbeta3 in complex with sibrafiban

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-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-MAN-MAN.1: 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)

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: 8 residues within 4Å: Chain B: N.99, S.369, F.370, N.371, P.381, S.398, I.399, E.400 No protein-ligand interaction detected (PLIP)

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

SO4.3: 6 residues within 4Å: Chain A: T.150, I.154, Y.155, N.158, S.161, W.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.161, A:S.161 SO4.4: 4 residues within 4Å: Chain A: F.10, P.410, F.411, Q.444 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.444 SO4.5: 3 residues within 4Å: Chain A: R.400, S.401, R.402 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.401, A:R.402 Water bridges: A:Q.395, A:R.400, A:R.400, A:S.401 Salt bridges: A:R.400, A:R.402 SO4.16: 4 residues within 4Å: Chain D: S.30, S.31, S.67, G.68 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.30, D:G.68 Water bridges: D:S.31

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: S.225, N.227, E.229, Y.230, W.260, R.276, R.279 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.227, A:E.229, A:R.276, A:R.279, A:R.279

6 x CA: CALCIUM ION(Non-covalent)

CA.7: 7 residues within 4Å: Chain A: E.243, F.244, 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:E.252, A:E.252 CA.8: 7 residues within 4Å: Chain A: D.297, V.298, N.299, D.301, R.303, D.305, L.332 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.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.365, A:D.367, A:D.369, A:Y.371, A:D.373 CA.10: 7 residues within 4Å: Chain A: D.426, I.427, D.428, N.430, Y.432, D.434, A.450 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.428, A:Y.432, A:D.434, A:D.434, H2O.1 CA.12: 6 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, M.335, D.336 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.123, B:D.126, B:D.127, H2O.21, H2O.24 CA.13: 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.11: 5 residues within 4Å: Chain B: S.121, S.123, N.215, E.220 Ligands: XQS.15 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.121, B:E.220, H2O.19, H2O.21, H2O.22

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

NAG.14: 5 residues within 4Å: Chain B: A.61, K.98, N.99, F.100, S.101 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.99

1 x XQS: sibrafiban (active form)(Non-covalent)

XQS.15: 18 residues within 4Å: Chain A: F.160, 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.11 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:Y.122, B:N.215, B:N.215, B:N.215, A:D.224, A:S.225 Water bridges: B:S.123, B:S.123 Hydrophobic interactions: A:F.160, A:Y.190, A:Y.190, A:L.192 pi-Stacking: A:F.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, F.Y. et al., A general chemical principle for creating closure-stabilizing integrin inhibitors. Cell (2022)

Release Date

2022-06-15

Peptides

Isoform 3 of Integrin alpha-IIb: A
Isoform Beta-3C of Integrin beta-3: B
Monoclonal antibody 10E5 heavy chain: C
Monoclonal antibody 10E5 light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Isoform 3 of Integrin alpha-IIb

Isoform Beta-3C of Integrin beta-3

Monoclonal antibody 10E5 heavy chain

Monoclonal antibody 10E5 light chain

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