SMTL ID : 7opp.1

Crystal structure of the Rab27a fusion with Slp2a-RBDa1 effector for SF4 pocket drug targeting

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

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

GNP.1: 25 residues within 4Å: Chain A: D.55, S.56, G.57, V.58, G.59, K.60, T.61, S.62, F.72, N.73, S.74, K.75, F.76, T.78, T.79, A.114, G.115, N.171, K.172, D.174, L.175, S.201, A.202, A.203 Ligands: MG.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:S.56, A:G.57, A:V.58, A:G.59, A:K.60, A:K.60, A:T.61, A:T.61, A:S.62, A:S.62, A:N.73, A:T.78, A:T.79, A:T.79, A:G.115, A:N.171, A:K.172, A:K.172, A:A.202, A:A.203 Water bridges: A:S.56, A:T.61, A:I.77, A:I.77, A:T.78 Salt bridges: A:D.174 pi-Stacking: A:F.72, A:F.72 pi-Cation interactions: A:K.172 GNP.3: 25 residues within 4Å: Chain B: D.55, S.56, G.57, V.58, G.59, K.60, T.61, S.62, F.72, N.73, S.74, K.75, F.76, T.78, T.79, A.114, G.115, N.171, K.172, D.174, L.175, S.201, A.202, A.203 Ligands: MG.4 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:S.56, B:G.57, B:V.58, B:G.59, B:K.60, B:K.60, B:T.61, B:T.61, B:S.62, B:S.62, B:N.73, B:T.78, B:T.79, B:T.79, B:T.113, B:G.115, B:N.171, B:K.172, B:K.172, B:A.202, B:A.203 Water bridges: B:T.61, B:L.116 Salt bridges: B:D.174 pi-Stacking: B:F.72, B:F.72 pi-Cation interactions: B:K.172

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.61, T.79, D.112 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.61, A:T.79, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain B: T.61, T.79 Ligands: GNP.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.61, B:T.79, H2O.8, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamshidiha, M. et al., Identification of the first structurally validated covalent ligands of the small GTPase RAB27A. Rsc Med Chem (2022)

Release Date

2022-04-06

Peptides

Synaptotagmin-like protein 2,Ras-related protein Rab-27A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Synaptotagmin-like protein 2,Ras-related protein Rab-27A