SMTL ID : 3zdz.2 (1 other biounit)

Integrin alphaIIB beta3 headpiece and RGD peptide complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x GLY- ARG- GLY- ASP- SER: RGD PEPTIDE(Non-covalent)

GLY-ARG-GLY-ASP-SER.1: 17 residues within 4Å: Chain A: F.160, Y.189, Y.190, L.192, F.231, D.232 Chain B: S.121, Y.122, S.123, S.213, R.214, N.215, R.216, D.217, A.218, E.220 Ligands: MN.10 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.121, B:Y.122, B:S.123, B:N.215, B:N.215, B:N.215, B:A.218, A:Y.190 Water bridges: B:S.123, A:F.160, A:D.224 pi-Cation interactions: A:F.231

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(Non-functional Binders)

NAG-NAG-BMA-MAN.2: 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)

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: 9 residues within 4Å: Chain B: N.99, S.369, F.370, N.371, P.381, S.398, I.399, E.400 Ligands: NAG.13 No protein-ligand interaction detected (PLIP)

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

SO4.4: 6 residues within 4Å: Chain A: F.87, A.89, R.90, H.112, K.124 Chain B: I.167 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.112, A:K.124

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

CL.5: 1 residues within 4Å: Chain A: Q.444 Ligand excluded by PLIP

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.7: 6 residues within 4Å: Chain A: D.297, 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.2 CA.8: 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.3 CA.9: 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:Y.432, A:D.434, H2O.4

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

MN.10: 5 residues within 4Å: Chain B: S.121, S.123, N.215, E.220 Ligands: GLY-ARG-GLY-ASP-SER.1 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.121, B:E.220, H2O.4, H2O.5 MN.11: 6 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, M.335, D.336 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.123, B:D.126, B:D.127, B:M.335, H2O.5 MN.12: 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

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

NAG.13: 7 residues within 4Å: Chain B: A.61, K.98, N.99, F.100, S.101 Ligands: NAG-NAG.3, NAG-NAG.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.98, B:N.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, J. et al., Complete Integrin Headpiece Opening in Eight Steps. J.Cell Biol. (2013)

Release Date

2013-06-05

Peptides

INTEGRIN ALPHA-IIB: A
INTEGRIN BETA-3: B
10E5 FAB HEAVY CHAIN: C
10E5 FAB LIGHT CHAIN: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

INTEGRIN ALPHA-IIB

INTEGRIN BETA-3

10E5 FAB HEAVY CHAIN

10E5 FAB LIGHT CHAIN

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