SMTL ID : 2hei.1

Crystal structure of human RAB5B in complex with GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 20 residues within 4Å: Chain A: E.16, S.17, A.18, V.19, G.20, K.21, S.22, S.23, F.33, E.35, Y.36, S.39, A.65, N.121, K.122, D.124, L.125, S.151, A.152, K.153 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.18, A:V.19, A:G.20, A:K.21, A:S.22, A:S.23, A:S.23, A:Y.36, A:S.39, A:N.121, A:K.122, A:K.122, A:A.152, A:K.153 Water bridges: A:S.23, A:H.34 Salt bridges: A:K.21, A:E.35, A:D.124 pi-Stacking: A:F.33, A:F.33 GDP.3: 20 residues within 4Å: Chain B: E.16, S.17, A.18, V.19, G.20, K.21, S.22, S.23, F.33, E.35, Y.36, S.39, A.65, N.121, K.122, D.124, L.125, S.151, A.152, K.153 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:A.18, B:V.19, B:G.20, B:K.21, B:S.22, B:S.23, B:S.23, B:Y.36, B:S.39, B:N.121, B:K.122, B:K.122, B:A.152, B:K.153 Water bridges: B:E.35, B:E.35, B:K.153 Salt bridges: B:K.21, B:E.35, B:D.124 pi-Stacking: B:F.33, B:F.33

2 x D1D: (4S,5S)-1,2-DITHIANE-4,5-DIOL(Non-covalent)

D1D.2: 11 residues within 4Å: Chain A: T.64, Q.67, E.68, Y.70, H.71, L.73, A.74, Y.77, Y.78, W.102, E.105 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.68, A:H.71, A:Y.78, A:W.102 Water bridges: A:T.64 D1D.4: 12 residues within 4Å: Chain B: L.14, T.64, Q.67, E.68, Y.70, H.71, L.73, A.74, Y.77, Y.78, W.102, E.105 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.71, B:E.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, B. et al., Crystal structure of human RAB5B in complex with GDP. To be Published

Release Date

2006-07-04

Peptides

Ras-related protein Rab-5B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ras-related protein Rab-5B