SMTL ID : 4cak.1

Three-dimensional reconstruction of intact human integrin alphaIIbbeta3 in a phospholipid bilayer nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 20.50 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain B: N.99 Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 26 residues within 4Å: Chain A: P.564, V.566, Q.595, C.608, V.609, P.610, Q.611, L.612, Q.613, A.638, N.639, E.640, G.641, E.642, G.643, M.693, K.694, K.695, N.696, A.697, Q.698 Chain B: M.387, N.449, N.450, G.451, N.452 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.638, A:Q.698 Hydrogen bonds: A:Q.613, A:E.640, A:E.640, A:E.640, A:E.640, A:E.642, A:E.642, A:N.696

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

NAG-NAG-BMA-MAN.2: 19 residues within 4Å: Chain A: E.229, W.260, S.261, W.262, T.263, L.264, R.281, G.282, E.283, Q.284, M.285, A.286, S.287 Chain B: K.253, N.316, L.317, Q.319, N.320, S.510 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.261, A:S.261, A:R.281, A:S.261, A:S.261, A:R.281, A:R.281

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 9 residues within 4Å: Chain A: V.599, L.600, D.601 Chain B: S.369, N.371, P.381, S.398, E.400 Ligands: NAG-NAG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.601, A:D.601

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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

NAG-NAG-BMA-MAN-MAN.5: 10 residues within 4Å: Chain B: V.529, T.554, Y.556, Y.557, N.559, D.627, E.628, N.629, T.630, R.633 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.556 Hydrogen bonds: B:T.630, B:R.633, B:E.628

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

NAG.6: 1 residues within 4Å: Chain A: N.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.15 NAG.7: 13 residues within 4Å: Chain A: N.2, L.3, D.4, D.367, S.404, Q.451, P.452, V.453, N.505, N.570, V.571, S.572, L.573 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.2 Hydrogen bonds: A:N.2, A:L.3, A:D.4, A:D.4, A:S.404, A:N.570

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, W.S. et al., Three-Dimensional Reconstruction of Intact Human Integrin Alphaiibbeta3; New Implications for Activation-Dependent Ligand Binding. Blood (2013)

Release Date

2013-10-30

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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