SMTL ID : 3bn3.1

crystal structure of ICAM-5 in complex with aL I domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 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: 5 residues within 4Å: Chain B: N.23, Q.46, R.50, W.51, A.53 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.26, B:R.50

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.12, S.14, T.79 Chain B: E.37 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:S.12, A:S.14, A:T.79, B:E.37, H2O.1, H2O.1

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

NAG.3: 3 residues within 4Å: Chain B: N.43, Q.55, V.57 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.57 Hydrogen bonds: B:S.19, B:Q.55 NAG.4: 3 residues within 4Å: Chain B: G.104, N.106, T.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.106 NAG.5: 2 residues within 4Å: Chain B: G.162, N.164 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.162 Water bridges: B:N.164, B:N.164, B:N.164 NAG.6: 6 residues within 4Å: Chain B: R.88, P.89, D.90, F.181, E.182, N.183 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.181 Hydrogen bonds: B:R.88, B:N.183

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain B: R.10, V.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.10 Water bridges: B:R.10 GOL.8: 6 residues within 4Å: Chain B: R.119, R.136, F.138, E.141, A.148, V.149 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.136, B:E.141, B:V.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., An unusual allosteric mobility of the C-terminal helix of a high-affinity alpha L integrin I domain variant bound to ICAM-5. Mol.Cell (2008)

Release Date

2008-08-19

Peptides

Integrin alpha-L: A
Intercellular adhesion molecule 5: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-L

Intercellular adhesion molecule 5