SMTL ID : 5hdb.1 (3 other biounits)

Integrin alphaIIbbeta3 in complex with Ro-435054

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-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 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.281, A:R.281, 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: 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)

3 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.401, A:S.401, A:R.402 Water bridges: A:R.402 Salt bridges: A:R.400, A:R.402

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: S.225, N.227, E.229, Y.230, R.276, R.279 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.279, A:R.279 Water bridges: A:S.225, A:S.225, A:Y.230, A:R.276, A:R.276, A:R.276

5 x CA: CALCIUM ION(Non-covalent)

CA.7: 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:D.245, A:D.247, A:T.250, A:E.252, A:E.252 CA.8: 6 residues within 4Å: Chain A: D.297, V.298, 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.9: 9 residues within 4Å: Chain A: D.365, L.366, D.367, R.368, 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: 5 interactions with chain A Metal complexes: A:D.426, A:D.428, A:Y.432, A:D.434, A:D.434 CA.12: 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: 5YB.14 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.121, B:S.123, B:E.220, H2O.13, H2O.13

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

NAG.13: 4 residues within 4Å: Chain B: A.61, K.98, N.99, F.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.98, B:N.99

1 x 5YB: N-(4-carbamimidoylbenzoyl)-beta-alanyl-L-alpha-aspartyl-L-phenylalanine(Non-covalent)

5YB.14: 21 residues within 4Å: Chain A: F.160, S.161, W.162, D.163, 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 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:Y.190, A:Y.190, A:Y.190, A:Y.190, A:L.192 Hydrogen bonds: A:D.224, B:Y.122, B:S.123, B:S.123, B:N.215, B:N.215, B:R.216 pi-Stacking: A:F.231 Water bridges: B:R.214, B:A.218, B:E.220

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

2016-02-03

Peptides

Integrin alpha-IIb: A
Integrin beta-3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-IIb

Integrin beta-3

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