SMTL ID : 4z7n.1 (1 other biounit)

Integrin alphaIIbbeta3 in complex with AGDV peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ALA- GLY- ASP- VAL: Tetrapeptide ALA-GLY-ASP-VAL(Non-covalent)

ALA-GLY-ASP-VAL.1: 12 residues within 4Å: Chain A: F.160, Y.190 Chain B: S.119, Y.120, S.121, R.212, N.213, R.214, D.215, A.216, E.218 Ligands: MN.13 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.120, B:S.121, B:S.121, B:N.213, B:N.213, B:R.214 Water bridges: B:S.121, B:E.218, A:F.160

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.2: 6 residues within 4Å: Chain A: W.262, R.281, M.285 Chain B: N.314, L.315, N.318 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.3: 7 residues within 4Å: Chain B: S.367, F.368, N.369, P.379, S.396, I.397, E.398 No protein-ligand interaction detected (PLIP)

4 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:D.245, A:D.247, A:T.250, A:T.250, A:E.252 CA.5: 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.301, A:R.303, A:D.305, A:D.305, H2O.1 CA.6: 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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.367, A:D.369, A:Y.371, A:D.373, H2O.1 CA.7: 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.426, A:D.428, A:D.434, A:D.434, H2O.1

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

SO4.8: 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 SO4.9: 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 SO4.10: 3 residues within 4Å: Chain A: R.400, S.401, R.402 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.401, A:S.401, A:S.401, A:R.402 Salt bridges: A:R.400, A:R.402 SO4.11: 3 residues within 4Å: Chain A: R.386, P.412, T.413 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.413, A:T.413 Salt bridges: A:R.386 SO4.17: 3 residues within 4Å: Chain D: S.30, S.67, G.68 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.30, D:G.68

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 6 residues within 4Å: Chain A: S.225, N.227, E.229, Y.230, R.276, R.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.276, A:R.279

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.13: 7 residues within 4Å: Chain B: S.119, S.121, N.213, E.218, D.249, A.250 Ligands: ALA-GLY-ASP-VAL.1 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.119, B:S.121, B:E.218, H2O.13, H2O.15 MN.14: 5 residues within 4Å: Chain B: S.121, M.122, D.124, D.125, D.249 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.121, B:D.124, B:D.249, H2O.15, H2O.20 MN.15: 7 residues within 4Å: Chain B: D.156, N.213, D.215, A.216, P.217, E.218, H.253 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.156, B:D.215, B:D.215, B:P.217, B:E.218

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

NAG.16: 4 residues within 4Å: Chain B: K.96, N.97, F.98, S.99 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, F.Y. et al., beta-Subunit Binding Is Sufficient for Ligands to Open the Integrin alpha IIb beta 3 Headpiece. J.Biol.Chem. (2016)

Release Date

2015-12-16

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

Related Entries With Identical Sequence