SMTL ID : 4nen.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-mer

Ligands

5 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.2: 2 residues within 4Å: Chain A: V.69, N.70 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: T.657, D.659, R.714, N.716, F.717, T.718, Y.741 Chain B: D.501 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.94, F.363, T.388 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.363 NAG-NAG.6: 4 residues within 4Å: Chain B: P.616, F.617, N.620, A.624 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.3: 11 residues within 4Å: Chain A: S.326, S.327, E.329, F.354, S.357, F.371, N.373, M.374, S.375, Q.376, N.378 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.329, A:S.326, A:S.327, A:S.327

5 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: D.511, V.512, 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.1 CA.8: 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:L.580, A:D.582, H2O.1 CA.9: 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.449, A:D.451, A:S.453, A:D.455 CA.12: 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.13: 3 residues within 4Å: Chain B: S.116, D.120, D.242 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.116, B:D.242, H2O.4, H2O.4, H2O.5

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain A: S.140, S.142, T.207, K.242 Ligands: CL.11 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.140, A:S.142, A:T.207, H2O.1, H2O.1 MG.14: 5 residues within 4Å: Chain A: E.318 Chain B: S.114, S.116, E.212, D.242 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:S.116, B:E.212, A:E.318, H2O.4, H2O.4

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

CL.11: 8 residues within 4Å: Chain A: S.140, G.141, S.142, G.205, F.206, T.207, E.244 Ligands: MG.10 Ligand excluded by PLIP

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

Related Entries With Identical Sequence