SMTL ID : 5e6u.1

Structures of leukocyte integrin aLb2: The aI domain, the headpiece, and the pocket for the internal ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.137, S.139, S.141, T.206, D.239 Ligands: CL.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.139, A:S.141, A:D.239, H2O.3, H2O.4 MG.6: 3 residues within 4Å: Chain B: D.112, S.114, E.212 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.114, B:E.212, H2O.16, H2O.19, H2O.19

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.443, D.445, D.447, E.449, E.451 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.443, A:D.445, A:D.447, A:E.449, H2O.6 CA.3: 6 residues within 4Å: Chain A: D.505, I.506, N.507, D.509, L.511, D.513 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.505, A:D.509, A:L.511, A:D.513, H2O.2 CA.7: 4 residues within 4Å: Chain B: S.116, D.119, D.120, E.325 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.116, B:D.119, B:D.120, B:E.325, H2O.17, H2O.24 CA.8: 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

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

CL.4: 4 residues within 4Å: Chain A: S.139, S.141, T.206 Ligands: MG.1 Ligand excluded by PLIP

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

NAG.5: 2 residues within 4Å: Chain A: N.64, Q.117 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.117 Water bridges: A:N.64, A:N.64, A:N.64 NAG.9: 4 residues within 4Å: Chain B: A.92, N.94, T.388, Q.390 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.390 NAG.10: 2 residues within 4Å: Chain B: R.143, N.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.143

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

2016-04-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-L

Integrin beta-2

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