SMTL ID : 4oi9.1

Crystal Structure of ICAM-5 D1-D4 ectodomain fragment, Space Group P21

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

3 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: 6 residues within 4Å: Chain A: N.23, S.25, Q.46, R.50, W.51 Ligands: EDO.25 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.50 NAG-NAG.2: 5 residues within 4Å: Chain A: D.90, R.91, V.92, N.183, S.184 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: Y.232, N.272, N.279 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-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-BMA-MAN.3: 2 residues within 4Å: Chain A: Q.268, N.285 No protein-ligand interaction detected (PLIP)

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

NAG.5: 3 residues within 4Å: Chain A: S.19, N.43, V.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.19 NAG.6: 4 residues within 4Å: Chain A: G.104, N.106, T.153, L.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.153 NAG.7: 2 residues within 4Å: Chain A: G.162, N.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.162, A:N.164 NAG.8: 3 residues within 4Å: Chain A: Q.338, L.339, N.340 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain A: I.364, N.366 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.364 Water bridges: A:N.366, A:N.366, A:N.366

31 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 7 residues within 4Å: Chain A: R.16, R.60, P.62, T.85, F.86, Q.87, R.146 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: R.119, F.138, A.148, V.149 Ligands: EDO.27 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: R.230, V.231, V.244 Ligands: EDO.40 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: Q.78, R.80 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: P.96, L.97, R.188, E.189 Ligands: EDO.26 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: R.174, G.177, L.178, G.179 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: D.198, A.199 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain A: V.11 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: S.19, L.20, Q.55 Ligand excluded by PLIP EDO.19: 1 residues within 4Å: Chain A: E.63 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: R.84, A.120, S.121, H.176 Ligands: EDO.35 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: T.123, R.135, E.170, D.172, R.174 Ligand excluded by PLIP EDO.22: 1 residues within 4Å: Chain A: R.60 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain A: R.41 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain A: A.293, K.365, R.367 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: W.21, Q.46 Ligands: NAG-NAG.1 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain A: L.97, P.98, P.99, E.189, L.190, R.191 Ligands: EDO.14 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: V.113, P.114, G.147, A.148, V.149 Ligands: EDO.11 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain A: E.182, N.183, S.184 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain A: R.201, T.219, L.220, D.221 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: L.133, T.153, V.154 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain A: S.349, S.368, A.369, E.370 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain A: R.201, L.202 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain A: A.315, G.316, P.334 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain A: A.120, G.140, E.141 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain A: R.84, H.176 Ligands: EDO.20 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain A: L.40, R.41, R.42 Ligands: EDO.38 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain A: R.47, G.48, W.51 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain A: L.36, T.38, L.40, R.42, R.54, L.56 Ligands: EDO.36 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain A: E.264, S.290 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain A: V.231, S.241, P.242, V.244 Ligands: EDO.12 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Recacha, R. et al., Crystal structures of an ICAM-5 ectodomain fragment show electrostatic-based homophilic adhesions. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-07-16

Peptides

Intercellular adhesion molecule 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Intercellular adhesion molecule 5

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