SMTL ID : 4neh.1

An internal ligand-bound, metastable state of a leukocyte integrin, aXb2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-1-1-mer

Ligands

4 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: 4 residues within 4Å: Chain A: S.929, H.930, V.931, N.1031 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: T.657, D.659, N.716, F.717, T.718, Y.741 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: A.92, N.94, F.363, R.371 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.363 Hydrogen bonds: B:R.371 NAG-NAG.6: 3 residues within 4Å: Chain B: N.620, A.623, A.624 No protein-ligand interaction detected (PLIP)

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.2: 3 residues within 4Å: Chain A: V.69, N.70, H.94 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN-MAN.3: 11 residues within 4Å: Chain A: S.325, S.327, E.329, F.354, S.357, F.371, N.373, M.374, S.375, Q.376, N.378 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.329, A:Q.376

5 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain A: D.574, T.576, D.578, L.580, D.582 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.574, A:T.576, A:D.578, A:L.580, H2O.1 CA.9: 5 residues within 4Å: Chain A: D.511, N.513, D.515, L.517, D.519 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.511, A:D.515, A:L.517, A:D.519, H2O.3 CA.10: 5 residues within 4Å: Chain A: D.447, D.449, D.451, S.453, D.455 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.447, A:D.451, A:D.451, A:S.453, A:D.455 CA.14: 5 residues within 4Å: Chain B: D.151, N.207, D.209, P.211, E.212 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.151, B:D.209, B:D.209, B:P.211, B:E.212 CA.15: 2 residues within 4Å: Chain B: D.120, E.325 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.120, B:E.325, H2O.9, H2O.11, H2O.11

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain A: S.140, S.142, T.207 Ligands: CL.12 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.140, A:S.142, A:T.207, H2O.2, H2O.3 MG.16: 5 residues within 4Å: Chain A: E.318 Chain B: S.114, S.116, E.212, D.242 6 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.318, B:S.114, B:S.116, B:E.212, H2O.9, H2O.10

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

NAG.11: 3 residues within 4Å: Chain A: T.801, N.880, S.882 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.880, A:S.882, A:S.882

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

CL.12: 7 residues within 4Å: Chain A: S.140, G.141, S.142, G.205, F.206, T.207 Ligands: MG.8 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 4 residues within 4Å: Chain A: F.328, G.352, T.355, W.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.355, A:W.356 Water bridges: A:G.352

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sen, M. et al., An internal ligand-bound, metastable state of a leukocyte integrin, alpha X beta 2. J.Cell Biol. (2013)

Release Date

2014-01-15

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-X

Integrin beta-2

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