SMTL ID : 3nid.1 (1 other biounit)

The Closed Headpiece of Integrin alphaIIB beta3 and its Complex with an alpahIIB beta3 -Specific Antagonist That Does Not Induce Opening

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-MAN-MAN-MAN.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: 5 residues within 4Å: Chain B: S.369, N.371, S.398, I.399, E.400 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: E.243, D.245, D.247, T.250, E.252 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.243, A:E.243, A:D.247, A:E.252, 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.365, A:D.367, A:D.369, A:Y.371, 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.15: 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:S.123, B:D.127, B:M.335, H2O.15, H2O.15 CA.16: 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

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: Q.395, S.401, R.402 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.395, A:S.401, A:S.401, A:R.402, A:R.402 GOL.8: 3 residues within 4Å: Chain A: F.160, Y.190 Ligands: GOL.11 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.159, A:Y.190 GOL.9: 5 residues within 4Å: Chain A: L.1, L.3, P.5, Q.405, V.454 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.1 GOL.10: 5 residues within 4Å: Chain A: A.89, R.90, H.112, K.124 Chain B: I.167 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:K.124, B:S.162 GOL.11: 4 residues within 4Å: Chain A: Y.190, L.192, F.231 Ligands: GOL.8 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.190 Water bridges: B:A.218 GOL.12: 2 residues within 4Å: Chain A: P.403, S.404 No protein-ligand interaction detected (PLIP) GOL.18: 7 residues within 4Å: Chain B: L.299, S.300, N.303, I.304, N.305, P.326, G.420 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.303, B:I.304, B:N.305

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

SO4.13: 4 residues within 4Å: Chain A: I.154, Y.155, N.158, S.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.161 SO4.19: 7 residues within 4Å: Chain B: Q.82, Q.106, Y.110, S.243, R.352, G.420, F.421 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.82 Water bridges: B:R.352, B:V.419 Salt bridges: B:R.352 SO4.20: 4 residues within 4Å: Chain C: K.38, R.40, E.46, F.64 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.38, C:R.40 SO4.21: 5 residues within 4Å: Chain D: Q.37, K.39, L.47, P.59, F.62 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.37 Water bridges: D:G.46 Salt bridges: D:K.39

1 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 3 residues within 4Å: Chain B: S.121, S.123, E.220 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.121, B:E.220, H2O.16, H2O.16, H2O.16

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

NAG.17: 4 residues within 4Å: Chain B: K.98, N.99, F.100, S.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.98, B:K.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, J.H. et al., Closed headpiece of integrin {alpha}IIb{beta}3 and its complex with an {alpha}IIb{beta}3-specific antagonist that does not induce opening. Blood (2010)

Release Date

2010-12-22

Peptides

Integrin alpha-IIb: A
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

Integrin alpha-IIb

Integrin beta-3

Monoclonal antibody 10E5 heavy chain

Monoclonal antibody 10E5 light chain

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