SMTL ID : 7eq2.2 (1 other biounit)

Crystal structure of GDP-bound Rab1a-T75D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

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

GDP.1: 20 residues within 4Å: Chain A: D.19, S.20, G.21, V.22, G.23, K.24, S.25, C.26, Y.36, E.38, E.71, R.72, N.124, K.125, D.127, L.128, S.154, A.155, K.156 Ligands: MG.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:G.21, A:V.22, A:G.23, A:K.24, A:S.25, A:C.26, A:Y.36, A:E.71, A:E.71, A:R.72, A:N.124, A:K.125, A:K.125, A:A.155, A:K.156 Water bridges: A:S.25, A:Y.36, A:E.38, A:E.38, A:I.41, A:T.67, A:R.72 Salt bridges: A:K.24, A:R.72, A:D.127 pi-Stacking: A:Y.36, A:Y.36

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.25 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.25, H2O.2, H2O.2, H2O.3, H2O.3

2 x NCO: COBALT HEXAMMINE(III)(Non-covalent)

NCO.3: 6 residues within 4Å: Chain A: D.110, R.111, Y.112, A.113, S.114, E.115 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.110, A:D.110, A:A.113, A:E.115, A:E.115 Water bridges: A:R.111, A:A.113 NCO.4: 3 residues within 4Å: Chain A: A.32, D.33, I.50 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.32, A:D.33, A:I.50 Water bridges: A:I.50, A:I.50, A:T.52

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 6 residues within 4Å: Chain A: K.13, W.65, S.79, Y.80, G.83, A.84 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.13, A:K.13, A:W.65, A:W.65, A:Y.80, A:A.84 Hydrogen bonds: A:S.79, A:Y.80, A:G.83

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.6: 2 residues within 4Å: Chain A: E.115, N.116 No protein-ligand interaction detected (PLIP) CAC.7: 3 residues within 4Å: Chain A: E.71, R.74, D.75 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, W. et al., Aurora kinase A-mediated phosphorylation triggers structural alteration of Rab1A to enhance ER complexity during mitosis. Nat.Struct.Mol.Biol. (2024)

Release Date

2022-11-02

Peptides

Ras-related protein Rab-1A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Ras-related protein Rab-1A

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