SMTL ID : 3dz8.1

Crystal structure of human Rab3B GTPase bound with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 15 residues within 4Å: Chain A: N.31, S.32, S.33, V.34, G.35, K.36, T.37, S.38, N.136, K.137, D.139, M.140, S.166, A.167, K.168 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:N.31, A:S.33, A:V.34, A:G.35, A:K.36, A:T.37, A:T.37, A:S.38, A:S.38, A:N.136, A:K.137, A:K.137, A:A.167, A:K.168 Water bridges: A:S.32, A:K.36, A:K.36, A:T.37, A:K.63, A:K.63 Salt bridges: A:K.36, A:D.139 GDP.8: 15 residues within 4Å: Chain B: N.31, S.32, S.33, V.34, G.35, K.36, T.37, S.38, N.136, K.137, D.139, M.140, S.166, A.167, K.168 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:N.31, B:S.33, B:V.34, B:G.35, B:K.36, B:T.37, B:S.38, B:S.38, B:N.136, B:K.137, B:K.137, B:A.167, B:K.168 Water bridges: B:S.32, B:K.36, B:K.36, B:T.37, B:T.37, B:K.63 Salt bridges: B:K.36, B:D.139

12 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 4 residues within 4Å: Chain A: S.32, D.78, T.79, A.80 No protein-ligand interaction detected (PLIP) UNX.3: 5 residues within 4Å: Chain A: A.44, D.45, T.49 Chain B: F.16, Q.17 No protein-ligand interaction detected (PLIP) UNX.4: 1 residues within 4Å: Chain B: T.87 No protein-ligand interaction detected (PLIP) UNX.5: 3 residues within 4Å: Chain A: T.47, R.67, R.174 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: N.170, R.174 No protein-ligand interaction detected (PLIP) UNX.7: 2 residues within 4Å: Chain A: R.67, H.68 No protein-ligand interaction detected (PLIP) UNX.9: 4 residues within 4Å: Chain B: S.32, D.78, T.79, A.80 No protein-ligand interaction detected (PLIP) UNX.10: 5 residues within 4Å: Chain A: F.16, Q.17 Chain B: A.44, D.45, T.49 No protein-ligand interaction detected (PLIP) UNX.11: 1 residues within 4Å: Chain A: T.87 No protein-ligand interaction detected (PLIP) UNX.12: 3 residues within 4Å: Chain B: T.47, R.67, R.174 No protein-ligand interaction detected (PLIP) UNX.13: 2 residues within 4Å: Chain B: N.170, R.174 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain B: R.67, H.68 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, Y. et al., Crystal structure of human Rab3B GTPase bound with GDP. To be Published

Release Date

2008-08-12

Peptides

Ras-related protein Rab-3B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ras-related protein Rab-3B