SMTL ID : 6l6o.1

Crystal structure of stabilized Rab5a GTPase domain from Leishmania donovani

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

GDP.1: 21 residues within 4Å: Chain A: E.23, S.24, G.25, A.26, G.27, K.28, S.29, S.30, F.40, L.41, A.42, N.43, E.75, N.128, K.129, D.131, L.132, S.159, A.160, K.161 Ligands: MG.4 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:E.23, A:G.25, A:A.26, A:G.27, A:K.28, A:S.29, A:S.30, A:S.30, A:L.41, A:N.43, A:N.128, A:K.129, A:K.129, A:S.159, A:A.160, A:K.161 Water bridges: A:S.29, A:S.29, A:S.29, A:S.29, A:Q.44, A:Q.44, A:T.71, A:E.75, A:K.161 Salt bridges: A:K.28, A:D.131 pi-Stacking: A:F.40, A:F.40

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: D.131, L.132, G.133, S.134, L.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.133, A:S.134

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 1 residues within 4Å: Chain A: R.145 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.145

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: S.29, D.70 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.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zohib, M. et al., Crystal structure of the GDP-bound GTPase domain of Rab5a from Leishmania donovani. Acta Crystallogr.,Sect.F (2020)

Release Date

2020-11-11

Peptides

Rab5a: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Rab5a

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