SMTL ID : 5ub8.1

Crystal structure of YPT31, a Rab family GTPase from Candida albicans, in complex with GDP and Zn(II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 21 residues within 4Å: Chain A: D.23, S.24, G.25, V.26, G.27, K.28, S.29, N.30, F.40, N.41, L.42, E.43, E.75, N.128, K.129, D.131, L.132, S.158, A.159, L.160 Ligands: ZN.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.25, A:V.26, A:G.27, A:K.28, A:S.29, A:N.30, A:N.30, A:N.41, A:E.43, A:E.43, A:E.75, A:N.128, A:K.129, A:K.129, A:A.159, A:L.160 Water bridges: A:K.28, A:S.29, A:S.29, A:T.71 Salt bridges: A:K.28, A:D.131 pi-Stacking: A:F.40, A:F.40 GDP.4: 21 residues within 4Å: Chain B: D.23, S.24, G.25, V.26, G.27, K.28, S.29, N.30, F.40, N.41, L.42, E.43, E.75, N.128, K.129, D.131, L.132, S.158, A.159, L.160 Ligands: ZN.5 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:G.25, B:V.26, B:G.27, B:K.28, B:S.29, B:N.30, B:N.30, B:N.41, B:E.43, B:E.43, B:E.43, B:E.75, B:E.75, B:N.128, B:K.129, B:K.129, B:A.159, B:L.160 Water bridges: B:K.28, B:S.29, B:S.29 Salt bridges: B:K.28, B:D.131 pi-Stacking: B:F.40, B:F.40

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: S.29, T.71 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.29, H2O.1, H2O.1, H2O.1, H2O.1 ZN.3: 2 residues within 4Å: Chain A: E.112, H.116 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.112, A:H.116, H2O.4 ZN.5: 3 residues within 4Å: Chain B: S.29, T.71 Ligands: GDP.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.29, H2O.6, H2O.6, H2O.6, H2O.6 ZN.6: 2 residues within 4Å: Chain B: E.112, H.116 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.112, B:H.116, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stogios, P.J., Crystal structure of YPT31, a Rab family GTPase from Candida albicans, in complex with GDP and Zn(II). To Be Published

Release Date

2017-01-11

Peptides

Likely rab family GTP-binding protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Likely rab family GTP-binding protein