SMTL ID : 2vdk.1

Re-refinement of Integrin AlphaIIbBeta3 Headpiece

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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

NAG-NAG-MAN-MAN-MAN.1: 5 residues within 4Å: Chain A: W.262, R.281, M.285 Chain B: L.317, N.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.281, A:R.281

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

NAG-NAG-MAN-MAN-MAN-MAN-MAN.2: 5 residues within 4Å: Chain B: S.369, N.371, S.398, I.399, E.400 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.400

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: F.87, A.89, R.90, H.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.90, A:K.124, A:K.124 GOL.11: 5 residues within 4Å: Chain B: D.126, D.127, D.251, N.313 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.126, B:N.313 Water bridges: B:D.126, B:D.126, B:D.251

6 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.5: 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.7 CA.6: 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.7: 5 residues within 4Å: Chain A: D.426, D.428, N.430, Y.432, D.434 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.426, A:D.428, A:Y.432, A:D.434, H2O.9 CA.13: 5 residues within 4Å: Chain B: S.123, D.126, D.127, D.251 Ligands: GOL.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.123, B:D.126, B:D.127, B:D.251, H2O.14 CA.14: 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

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

NAG.8: 1 residues within 4Å: Chain A: N.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.15 Water bridges: A:N.15 NAG.9: 1 residues within 4Å: Chain A: N.249 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain B: N.99, S.398 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.99

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.10: 9 residues within 4Å: Chain B: S.121, Y.122, S.123, R.214, N.215, R.216, D.217, E.220 Ligands: MG.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.122, B:S.123, B:N.215, B:N.215 Water bridges: B:S.121, B:S.123

1 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 4 residues within 4Å: Chain B: S.121, S.123, E.220 Ligands: CAC.10 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Springer, T.A. et al., Structural Basis for Distinctive Recognition of Fibrinogen Gammac Peptide by the Platelet Integrin Alphaiibbeta3. J.Cell Biol. (2008)

Release Date

2008-09-02

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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