SMTL ID : 5es4.3 (3 other biounits)

RE-REFINEMENT OF INTEGRIN ALPHAXBETA2 ECTODOMAIN IN THE CLOSED/BENT CONFORMATION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[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-MAN.1: 6 residues within 4Å: Chain A: I.38, N.42, Q.43, T.44, N.70 Chain B: K.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.272, B:K.272

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: 8 residues within 4Å: Chain A: E.329, F.354, S.357, F.371, N.373, M.374, S.375, Q.376 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.329

1 x NAG- NAG- BMA- MAN: 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.3: 7 residues within 4Å: Chain A: T.657, D.659, N.716, F.717, T.718, Y.741 Chain B: D.501 No protein-ligand interaction detected (PLIP)

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.4: 4 residues within 4Å: Chain A: S.841, N.880, S.882, T.887 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.447, D.449, D.451, S.453, D.455 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.451, A:S.453, A:D.455, A:D.455, H2O.1 CA.6: 6 residues within 4Å: Chain A: D.511, V.512, N.513, D.515, L.517, D.519 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.511, A:D.515, A:L.517, A:D.519 CA.7: 5 residues within 4Å: Chain A: D.574, T.576, D.578, L.580, D.582 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.574, A:T.576, A:D.578, A:L.580, A:D.582 CA.12: 4 residues within 4Å: Chain B: S.116, D.120, D.242, E.325 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.116, B:D.120, B:E.325

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

NAG.8: 4 residues within 4Å: Chain A: S.929, H.930, V.931, N.1031 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.929, A:H.930, A:V.931 NAG.9: 2 residues within 4Å: Chain A: N.42, E.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.96 NAG.10: 1 residues within 4Å: Chain A: N.678 No protein-ligand interaction detected (PLIP) NAG.11: 5 residues within 4Å: Chain A: Y.918, N.920, S.922, E.925 Chain B: V.674 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.922, A:S.922, A:S.922 NAG.13: 1 residues within 4Å: Chain B: N.94 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain B: S.141, R.143, N.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.141 NAG.15: 4 residues within 4Å: Chain B: P.616, F.617, G.618, N.620 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sen, M. et al., Leukocyte integrin alpha L beta 2 headpiece structures: The alpha I domain, the pocket for the internal ligand, and concerted movements of its loops. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-03-02

Peptides

Integrin alpha-X: A
Integrin beta-2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Integrin alpha-X

Integrin beta-2

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