SMTL ID : 1r2q.1

Crystal Structure of Human Rab5a GTPase Domain at 1.05 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.20, T.38 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.20, A:T.38, H2O.1, H2O.2

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.2: 25 residues within 4Å: Chain A: E.14, S.15, A.16, V.17, G.18, K.19, S.20, S.21, F.31, H.32, E.33, Q.35, S.37, T.38, A.63, G.64, N.119, K.120, D.122, L.123, S.149, A.150, K.151 Ligands: MG.1, GOL.3 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:S.15, A:A.16, A:V.17, A:G.18, A:K.19, A:K.19, A:S.20, A:S.20, A:S.21, A:S.21, A:H.32, A:T.38, A:T.62, A:G.64, A:N.119, A:K.120, A:K.120, A:A.150, A:K.151 Water bridges: A:E.33, A:E.33, A:E.36, A:T.38, A:T.38, A:Q.65, A:Q.65, A:K.151 Salt bridges: A:D.122 pi-Stacking: A:F.31, A:F.31

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: A.16, Q.35 Ligands: GNP.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.35 Water bridges: A:A.16 GOL.4: 3 residues within 4Å: Chain A: T.89, K.126 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.126 GOL.5: 4 residues within 4Å: Chain A: E.92, A.95, R.96, N.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.92, A:R.96, A:N.99 GOL.6: 2 residues within 4Å: Chain A: R.106, Q.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.107 GOL.7: 6 residues within 4Å: Chain A: D.87, T.89, K.120, L.123, K.126 Ligands: GOL.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.87, A:K.126 Water bridges: A:D.87, A:D.87, A:T.89, A:K.120, A:K.120 GOL.8: 6 residues within 4Å: Chain A: Q.105, P.110, I.112, I.114, N.141, S.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105, A:I.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Terzyan, S. et al., Refinement of the structure of human Rab5a GTPase domain at 1.05 A resolution. Acta Crystallogr.,Sect.D (2004)

Release Date

2003-12-23

Peptides

Ras-related protein Rab-5A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ras-related protein Rab-5A

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