SMTL ID : 5e6s.4 (3 other biounits)

Structures of leukocyte integrin aLB2: The aI domain, the headpiece, and the pocket for the internal ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-3-3-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.137, S.139, S.141, T.206, D.239 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.139, A:S.141, A:D.239, H2O.2, H2O.4 MG.10: 4 residues within 4Å: Chain C: S.139, S.141, T.206, D.239 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.139, C:S.141, C:D.239, H2O.29, H2O.40 MG.19: 4 residues within 4Å: Chain E: S.139, S.141, T.206, D.239 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.139, E:S.141, E:D.239, H2O.64, H2O.65

15 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.443, D.447, E.449, E.451 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.443, A:D.447, A:E.451, H2O.5, H2O.9 CA.3: 5 residues within 4Å: Chain A: D.505, 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.4 CA.4: 6 residues within 4Å: Chain A: D.565, L.566, E.567, D.569, L.571, D.573 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.565, A:D.569, A:D.573, H2O.6 CA.6: 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.22, H2O.26 CA.7: 6 residues within 4Å: Chain B: D.151, F.157, N.207, D.209, P.211, E.212 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.151, B:D.209, B:D.209, B:P.211 CA.11: 4 residues within 4Å: Chain C: D.443, D.447, E.449, E.451 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.443, C:E.449, C:E.451, H2O.28, H2O.30 CA.12: 5 residues within 4Å: Chain C: D.505, N.507, D.509, L.511, D.513 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.505, C:D.509, C:L.511, C:D.513, H2O.29 CA.13: 5 residues within 4Å: Chain C: D.565, D.569, L.571, D.573, S.586 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.569, C:D.573, C:D.573, H2O.27 CA.15: 4 residues within 4Å: Chain D: S.116, D.119, D.120, E.325 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.116, D:D.119, D:D.120, D:E.325, H2O.47, H2O.53 CA.16: 7 residues within 4Å: Chain D: D.151, F.157, N.207, D.209, P.211, E.212, H.246 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.151, D:D.209, D:D.209, D:P.211 CA.20: 4 residues within 4Å: Chain E: D.443, D.447, E.449, E.451 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.443, E:E.449, E:E.451, H2O.55, H2O.56 CA.21: 5 residues within 4Å: Chain E: D.505, N.507, D.509, L.511, D.513 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.505, E:D.509, E:L.511, E:D.513, H2O.56 CA.22: 4 residues within 4Å: Chain E: D.565, D.569, L.571, D.573 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.565, E:D.569, E:D.573, E:D.573, H2O.66 CA.24: 5 residues within 4Å: Chain F: S.116, M.117, D.119, D.120, E.325 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:S.116, F:D.119, F:E.325, H2O.76, H2O.77 CA.25: 6 residues within 4Å: Chain F: D.151, F.157, N.207, D.209, P.211, E.212 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.151, F:D.209, F:D.209, F:P.211

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

NAG.5: 3 residues within 4Å: Chain A: N.64, L.103, Q.117 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.103 Hydrogen bonds: A:N.64 NAG.8: 2 residues within 4Å: Chain B: N.94, F.363 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.363 NAG.9: 2 residues within 4Å: Chain B: R.143, N.190 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.190 Water bridges: B:R.143, B:N.190 NAG.14: 4 residues within 4Å: Chain C: N.64, L.103, Q.117, R.119 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.103 NAG.17: 3 residues within 4Å: Chain D: A.92, N.94, Q.390 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.94 NAG.18: 2 residues within 4Å: Chain D: R.143, N.190 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.143 NAG.23: 4 residues within 4Å: Chain E: N.64, L.103, Q.117, R.119 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.64, E:Q.117, E:R.119 Water bridges: E:K.252, E:K.252 NAG.26: 5 residues within 4Å: Chain F: A.92, N.94, F.363, T.388, Q.390 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.390 NAG.27: 2 residues within 4Å: Chain F: R.143, N.190 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.190 Water bridges: F:N.190

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-L: ACE
Integrin beta-2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
E

E
C

B
B

D
F

F
D

Integrin alpha-L

Integrin beta-2

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