SMTL ID : 3k72.3 (2 other biounits)

Structure of integrin alphaX beta2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

hetero-4-4-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: A.40, A.41, N.42 Chain B: H.161 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: A.40, A.41, N.42 Chain D: H.161 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain E: A.40, A.41, N.42 Chain F: H.161 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain G: A.40, A.41, N.42 Chain H: H.161 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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(Non-covalent)

NAG-NAG-MAN-MAN-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-MAN-MAN.6: 5 residues within 4Å: Chain C: F.354, N.373, S.375, Q.376 Ligands: MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN-MAN.25: 5 residues within 4Å: Chain E: E.329, F.354, N.373, S.375, Q.376 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN-MAN.29: 5 residues within 4Å: Chain G: F.354, N.373, S.375, Q.376 Ligands: MAN.38 No protein-ligand interaction detected (PLIP)

6 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.3: 4 residues within 4Å: Chain A: T.657, D.659, N.716, Y.741 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.4: 5 residues within 4Å: Chain A: T.801, V.834, N.880, S.882, T.887 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.7: 4 residues within 4Å: Chain C: T.657, D.659, N.716, Y.741 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.26: 4 residues within 4Å: Chain E: T.657, D.659, N.716, Y.741 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.27: 5 residues within 4Å: Chain E: T.801, V.834, N.880, S.882, T.887 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.30: 4 residues within 4Å: Chain G: T.657, D.659, N.716, Y.741 No protein-ligand interaction detected (PLIP)

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

NAG.8: 3 residues within 4Å: Chain A: T.676, N.678, R.679 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.676 NAG.12: 2 residues within 4Å: Chain B: A.92, N.94 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain B: N.479 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.479 NAG.16: 3 residues within 4Å: Chain C: T.676, N.678, R.679 No protein-ligand interaction detected (PLIP) NAG.17: 5 residues within 4Å: Chain C: T.801, V.834, N.880, T.887, K.892 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.887 NAG.21: 2 residues within 4Å: Chain D: A.92, N.94 No protein-ligand interaction detected (PLIP) NAG.23: 1 residues within 4Å: Chain D: N.479 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.479 NAG.31: 3 residues within 4Å: Chain E: T.676, N.678, R.679 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.676 NAG.35: 2 residues within 4Å: Chain F: A.92, N.94 No protein-ligand interaction detected (PLIP) NAG.37: 1 residues within 4Å: Chain F: N.479 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.479 NAG.39: 3 residues within 4Å: Chain G: T.676, N.678, R.679 No protein-ligand interaction detected (PLIP) NAG.40: 5 residues within 4Å: Chain G: T.801, V.834, N.880, T.887, K.892 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:T.887 NAG.44: 2 residues within 4Å: Chain H: A.92, N.94 No protein-ligand interaction detected (PLIP) NAG.46: 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.9: 6 residues within 4Å: Chain A: D.447, V.448, D.449, D.451, S.453, D.455 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.447, A:D.449, A:S.453, A:D.455 CA.10: 8 residues within 4Å: Chain A: D.511, V.512, N.513, G.514, D.515, L.517, T.518, D.519 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.517 CA.11: 6 residues within 4Å: Chain A: D.574, T.576, D.578, L.580, V.581, 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.13: 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.18: 6 residues within 4Å: Chain C: D.447, V.448, D.449, D.451, S.453, D.455 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.447, C:D.449, C:S.453, C:D.455 CA.19: 8 residues within 4Å: Chain C: D.511, V.512, N.513, G.514, D.515, L.517, T.518, D.519 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:L.517 CA.20: 5 residues within 4Å: Chain C: D.574, T.576, 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.22: 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.32: 6 residues within 4Å: Chain E: D.447, V.448, D.449, D.451, S.453, D.455 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.447, E:D.449, E:S.453, E:D.455 CA.33: 8 residues within 4Å: Chain E: D.511, V.512, N.513, G.514, D.515, L.517, T.518, D.519 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:L.517 CA.34: 6 residues within 4Å: Chain E: D.574, T.576, D.578, L.580, V.581, 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.41: 6 residues within 4Å: Chain G: D.447, V.448, D.449, D.451, S.453, D.455 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.447, G:D.449, G:S.453, G:D.455 CA.42: 8 residues within 4Å: Chain G: D.511, V.512, N.513, G.514, D.515, L.517, T.518, D.519 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:L.517 CA.43: 5 residues within 4Å: Chain G: D.574, T.576, 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

2 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.15: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) MAN.38: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN-MAN.29 No protein-ligand interaction detected (PLIP)

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
A

G
C

B
B

D
D

F
B

H
D

Integrin alpha-X

Integrin beta-2

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