SMTL ID : 3k6s.5 (4 other biounits)

Structure of integrin alphaXbeta2 ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-4-4-mer

Ligands

9 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: 3 residues within 4Å: Chain A: A.40, A.41, N.42 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: T.657, D.659, N.716, T.718, Y.741 Chain B: D.501 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: A.40, A.41, N.42 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: F.354, N.373, Q.376 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain C: T.657, D.659, N.716, T.718, Y.741 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain E: A.40, A.41, N.42 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 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.10: 3 residues within 4Å: Chain G: A.40, A.41, N.42 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain G: T.657, D.659, N.716, T.718, Y.741 Chain H: D.501 No protein-ligand interaction detected (PLIP)

1 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

NAG-NAG-MAN-MAN-MAN.2: 5 residues within 4Å: Chain A: D.230, F.354, N.373, Q.376 Ligands: MAN.13 No protein-ligand interaction detected (PLIP)

2 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

NAG-NAG-MAN.8: 3 residues within 4Å: Chain E: F.354, N.373, Q.376 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.11: 3 residues within 4Å: Chain G: F.354, N.373, Q.376 No protein-ligand interaction detected (PLIP)

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.13: 3 residues within 4Å: Chain A: D.230, A.231 Ligands: NAG-NAG-MAN-MAN-MAN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.230, A:A.231

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

NAG.14: 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.15: 4 residues within 4Å: Chain A: T.801, V.834, N.880, T.887 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.887 NAG.20: 2 residues within 4Å: Chain B: A.92, N.94 No protein-ligand interaction detected (PLIP) NAG.22: 3 residues within 4Å: Chain C: T.676, N.678, R.679 No protein-ligand interaction detected (PLIP) NAG.23: 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.27: 2 residues within 4Å: Chain D: A.92, N.94 No protein-ligand interaction detected (PLIP) NAG.29: 3 residues within 4Å: Chain E: T.676, N.678, R.679 No protein-ligand interaction detected (PLIP) NAG.30: 4 residues within 4Å: Chain E: T.801, V.834, N.880, T.887 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.36: 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.37: 4 residues within 4Å: Chain G: T.801, V.834, N.880, T.887 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:T.887 NAG.41: 2 residues within 4Å: Chain H: A.92, N.94 No protein-ligand interaction detected (PLIP)

16 x CA: CALCIUM ION(Non-covalent)

CA.16: 6 residues within 4Å: Chain A: D.447, 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.17: 7 residues within 4Å: Chain A: D.511, V.512, N.513, G.514, D.515, L.517, D.519 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.517 CA.18: 6 residues within 4Å: Chain A: D.574, T.576, Q.577, D.578, L.580, D.582 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.574, A:T.576, A:D.578, A:L.580, A:D.582 CA.21: 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.24: 6 residues within 4Å: Chain C: D.447, D.449, D.451, S.453, T.454, D.455 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.447, C:D.451, C:S.453 CA.25: 7 residues within 4Å: Chain C: D.511, V.512, N.513, G.514, D.515, L.517, D.519 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:L.517 CA.26: 6 residues within 4Å: Chain C: D.574, T.576, Q.577, D.578, L.580, D.582 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.574, C:T.576, 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: 6 residues within 4Å: Chain E: D.447, D.449, D.451, S.453, T.454, D.455 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.447, E:D.451, E:S.453 CA.32: 7 residues within 4Å: Chain E: D.511, V.512, N.513, G.514, D.515, L.517, D.519 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:L.517 CA.33: 6 residues within 4Å: Chain E: D.574, T.576, Q.577, D.578, L.580, D.582 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.574, E:T.576, E:D.578, E:L.580, E:D.582 CA.35: 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.38: 6 residues within 4Å: Chain G: D.447, D.449, D.451, S.453, T.454, D.455 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.447, G:D.451, G:S.453 CA.39: 7 residues within 4Å: Chain G: D.511, V.512, N.513, G.514, D.515, L.517, D.519 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:L.517 CA.40: 6 residues within 4Å: Chain G: D.574, T.576, Q.577, D.578, L.580, D.582 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.574, G:T.576, G:D.578, G:L.580, G:D.582 CA.42: 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.19: 4 residues within 4Å: Chain A: D.138, S.140, S.142, D.240 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.140, A:S.142, A:D.240, 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

Related Entries With Identical Sequence