SMTL ID : 3k71.5 (4 other biounits)

Structure of integrin alphaX beta2 ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.95 Å

Oligo State

hetero-4-4-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: A.40, A.41, N.42 Chain B: H.161 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: A.40, A.41, N.42 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: F.354, N.373, S.375, Q.376 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain E: A.40, A.41, N.42 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain G: A.40, A.41, N.42 No protein-ligand interaction detected (PLIP)

7 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG-MAN.2: 5 residues within 4Å: Chain A: E.329, F.354, N.373, S.375, Q.376 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.3: 5 residues within 4Å: Chain A: T.657, D.659, N.716, Y.741 Chain B: D.501 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.4: 4 residues within 4Å: Chain A: S.803, V.834, T.878, N.880 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.7: 6 residues within 4Å: Chain C: T.657, D.659, N.716, T.718, Y.741 Chain D: D.501 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 5 residues within 4Å: Chain E: F.354, F.371, N.373, S.375, Q.376 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 6 residues within 4Å: Chain E: T.657, D.659, N.716, T.718, Y.741 Chain F: D.501 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.13: 5 residues within 4Å: Chain G: T.657, D.659, N.716, Y.741 Chain H: D.501 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-MAN-MAN.12: 4 residues within 4Å: Chain G: F.354, N.373, S.375, Q.376 No protein-ligand interaction detected (PLIP)

15 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.14: 2 residues within 4Å: Chain A: T.676, N.678 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.676 NAG.18: 2 residues within 4Å: Chain B: A.92, N.94 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain B: N.479, N.480 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.479, B:N.480 NAG.21: 3 residues within 4Å: Chain C: T.676, N.678, R.679 No protein-ligand interaction detected (PLIP) NAG.22: 4 residues within 4Å: Chain C: T.801, V.834, N.880, T.887 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.887 NAG.26: 2 residues within 4Å: Chain D: A.92, N.94 No protein-ligand interaction detected (PLIP) NAG.27: 1 residues within 4Å: Chain D: N.479 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.479 NAG.29: 3 residues within 4Å: Chain E: T.676, N.678, R.679 No protein-ligand interaction detected (PLIP) NAG.30: 5 residues within 4Å: Chain E: T.801, V.834, N.880, T.887, K.892 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:T.887 NAG.34: 2 residues within 4Å: Chain F: A.92, N.94 No protein-ligand interaction detected (PLIP) NAG.35: 1 residues within 4Å: Chain F: N.479 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.479 NAG.37: 3 residues within 4Å: Chain G: T.676, N.678, R.679 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:T.676 NAG.38: 3 residues within 4Å: Chain G: T.801, N.880, T.887 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:T.887 NAG.43: 2 residues within 4Å: Chain H: A.92, N.94 No protein-ligand interaction detected (PLIP) NAG.44: 1 residues within 4Å: Chain H: N.479 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.479

16 x CA: CALCIUM ION(Non-covalent)

CA.15: 7 residues within 4Å: Chain A: D.447, V.448, D.449, D.451, S.453, T.454, D.455 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.447, A:S.453 CA.16: 8 residues within 4Å: Chain A: D.511, V.512, N.513, G.514, D.515, K.516, L.517, T.518 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.515, A:L.517 CA.17: 7 residues within 4Å: Chain A: D.574, L.575, T.576, Q.577, D.578, L.580, D.582 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.574, A:D.578, A:D.578, A:L.580, A:D.582 CA.20: 5 residues within 4Å: Chain B: S.116, M.117, D.119, D.120, E.325 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.116, B:D.119, B:D.120, B:E.325, B:E.325 CA.23: 7 residues within 4Å: Chain C: D.447, V.448, D.449, D.451, S.453, T.454, D.455 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.447, C:S.453 CA.24: 8 residues within 4Å: Chain C: D.511, V.512, N.513, G.514, D.515, K.516, L.517, T.518 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.515, C:L.517 CA.25: 7 residues within 4Å: Chain C: D.574, L.575, T.576, Q.577, D.578, L.580, D.582 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.574, C:D.578, C:D.578, C:L.580, C:D.582 CA.28: 5 residues within 4Å: Chain D: S.116, M.117, D.119, D.120, E.325 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:S.116, D:D.119, D:D.120, D:E.325, D:E.325 CA.31: 7 residues within 4Å: Chain E: D.447, V.448, D.449, D.451, S.453, T.454, D.455 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.447, E:S.453 CA.32: 8 residues within 4Å: Chain E: D.511, V.512, N.513, G.514, D.515, K.516, L.517, T.518 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.515, E:L.517 CA.33: 7 residues within 4Å: Chain E: D.574, L.575, T.576, Q.577, D.578, L.580, D.582 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.574, E:D.578, E:D.578, E:L.580, E:D.582 CA.36: 5 residues within 4Å: Chain F: S.116, M.117, D.119, D.120, E.325 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:S.116, F:D.119, F:D.120, F:E.325, F:E.325 CA.39: 7 residues within 4Å: Chain G: D.447, V.448, D.449, D.451, S.453, T.454, D.455 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.447, G:S.453 CA.40: 8 residues within 4Å: Chain G: D.511, V.512, N.513, G.514, D.515, K.516, L.517, T.518 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.515, G:L.517 CA.41: 7 residues within 4Å: Chain G: D.574, L.575, T.576, Q.577, D.578, L.580, D.582 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.574, G:D.578, G:D.578, G:L.580, G:D.582 CA.45: 5 residues within 4Å: Chain H: S.116, M.117, D.119, D.120, E.325 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:S.116, H:D.119, H:D.120, H:E.325, H:E.325

1 x MG: MAGNESIUM ION(Non-covalent)

MG.42: 6 residues within 4Å: Chain G: D.138, S.140, S.142, T.207, D.240, G.241 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:S.140, G:S.142, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, C. et al., Structure of an integrin with an alphaI domain, complement receptor type 4. Embo J. (2010)

Release Date

2010-01-12

Peptides

Integrin alpha-X: ACEG
Integrin beta-2: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

Integrin alpha-X

Integrin beta-2

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