SMTL ID : 7l8p.3 (2 other biounits)

Integrin alphaIIbbeta3 in complex with sibrafiban

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-2-2-2-2-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)

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: 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) NAG-NAG.4: 9 residues within 4Å: Chain D: N.99, S.369, F.370, N.371, P.381, S.398, I.399, E.400 Ligands: NAG.31 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-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-MAN.3: 6 residues within 4Å: Chain C: W.262, R.281, M.285 Chain D: N.316, L.317, N.320 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.281, C:R.281 Hydrogen bonds: C:R.281

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

SO4.5: 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 SO4.6: 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 SO4.7: 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 SO4.18: 7 residues within 4Å: Chain C: F.87, A.89, R.90, H.112, K.124 Chain D: S.162, I.167 4 PLIP interactions: 4 interactions with chain C Water bridges: C:H.112, C:H.112 Salt bridges: C:H.112, C:K.124 SO4.19: 4 residues within 4Å: Chain C: Q.395, R.400, S.401, R.402 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.401, C:R.402 Water bridges: C:Q.395, C:R.402, C:R.402 Salt bridges: C:R.400, C:R.402 SO4.20: 5 residues within 4Å: Chain C: S.225, N.227, Y.230, R.276, R.279 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.227, C:R.279 Salt bridges: C:R.276 SO4.32: 4 residues within 4Å: Chain H: S.30, S.31, S.67, G.68 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:S.30, H:G.68 Water bridges: H:S.31

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 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

12 x CA: CALCIUM ION(Non-covalent)

CA.9: 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.10: 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.11: 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.12: 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.14: 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.15: 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.23: 7 residues within 4Å: Chain C: E.243, D.245, D.247, L.248, T.250, T.251, E.252 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.243, C:D.245, C:T.250, C:T.250, C:E.252 CA.24: 7 residues within 4Å: Chain C: D.297, V.298, N.299, D.301, R.303, D.305, L.332 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.301, C:R.303, C:D.305, C:D.305, H2O.29 CA.25: 8 residues within 4Å: Chain C: D.365, L.366, D.367, D.369, Y.371, D.373, L.393, G.394 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.365, C:D.367, C:D.369, C:Y.371, C:D.373 CA.26: 7 residues within 4Å: Chain C: D.426, I.427, D.428, N.430, Y.432, D.434, A.450 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.426, C:D.428, C:Y.432, C:D.434, C:D.434 CA.29: 6 residues within 4Å: Chain D: S.123, M.124, D.126, D.127, M.335, D.336 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.123, D:D.127, D:M.335, H2O.39, H2O.44 CA.30: 6 residues within 4Å: Chain D: D.158, N.215, D.217, P.219, E.220, H.255 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.158, D:D.217, D:D.217, D:P.219, D:E.220

2 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 5 residues within 4Å: Chain B: S.121, S.123, N.215, E.220 Ligands: XQS.17 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 MG.28: 6 residues within 4Å: Chain D: S.121, S.123, N.215, E.220, A.252 Ligands: XQS.27 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.121, D:E.220, H2O.39, H2O.40, H2O.40

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

NAG.16: 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 NAG.31: 6 residues within 4Å: Chain D: A.61, K.98, N.99, F.100, S.101 Ligands: NAG-NAG.4 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.98, D:N.99

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

XQS.17: 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.13 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 XQS.27: 19 residues within 4Å: Chain C: F.160, Y.189, Y.190, L.192, D.224, S.225, S.226, F.231 Chain D: S.121, Y.122, S.123, Y.166, R.214, N.215, R.216, D.217, A.218, E.220 Ligands: MG.28 14 PLIP interactions: 6 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:Y.122, D:N.215, D:N.215, D:N.215, C:D.224, C:S.225 Water bridges: D:S.123, D:A.218 Hydrophobic interactions: C:F.160, C:Y.190, C:Y.190, C:Y.190, C:L.192 pi-Stacking: C:F.231

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.21: 2 residues within 4Å: Chain C: F.411, Q.444 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain C: W.58, A.60, D.428 Ligand excluded by PLIP

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: AC
Isoform Beta-3C of Integrin beta-3: BD
Monoclonal antibody 10E5 heavy chain: EG
Monoclonal antibody 10E5 light chain: FH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

G
H

F
F

H
L

Isoform 3 of Integrin alpha-IIb

Isoform Beta-3C of Integrin beta-3

Monoclonal antibody 10E5 heavy chain

Monoclonal antibody 10E5 light chain

Related Entries With Identical Sequence