SMTL ID : 7opr.1

Rab27a fusion with Slp2a-RBDa1 effector covalent adduct with CB1 in C123

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

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

GNP.1: 24 residues within 4Å: Chain A: S.55, G.56, V.57, G.58, K.59, T.60, S.61, F.71, N.72, S.73, K.74, F.75, T.77, T.78, A.113, G.114, N.170, K.171, D.173, L.174, S.200, A.201, A.202 Ligands: MG.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:G.56, A:V.57, A:G.58, A:K.59, A:K.59, A:T.60, A:S.61, A:S.61, A:N.72, A:T.77, A:T.78, A:T.78, A:G.114, A:N.170, A:K.171, A:K.171, A:A.201, A:A.202 Water bridges: A:S.55, A:T.60, A:I.76, A:T.77, A:T.78, A:L.115 Salt bridges: A:D.173 pi-Stacking: A:F.71, A:F.71 pi-Cation interactions: A:K.171 GNP.11: 26 residues within 4Å: Chain B: D.54, S.55, G.56, V.57, G.58, K.59, T.60, S.61, F.71, N.72, S.73, K.74, F.75, T.77, T.78, A.113, G.114, N.170, K.171, D.173, L.174, S.200, A.201, A.202 Ligands: MG.12, GOL.13 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:S.55, B:G.56, B:V.57, B:G.58, B:K.59, B:K.59, B:T.60, B:T.60, B:S.61, B:S.61, B:N.72, B:T.78, B:G.114, B:N.170, B:K.171, B:K.171, B:A.201, B:A.202 Water bridges: B:S.55, B:I.76, B:T.77, B:T.78, B:T.78 Salt bridges: B:D.173 pi-Stacking: B:F.71, B:F.71 pi-Cation interactions: B:K.171

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.60, T.78, D.111 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.60, A:T.78, H2O.1, H2O.2 MG.12: 4 residues within 4Å: Chain B: T.60, T.78, D.111 Ligands: GNP.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.60, B:T.78, H2O.7, H2O.8

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: S.172, D.173, N.203, T.205 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.172, A:N.203, A:T.205, A:T.205 GOL.4: 6 residues within 4Å: Chain A: D.54, R.119, N.146, N.149, W.150, Q.153 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.119, A:R.119, A:Q.153 Water bridges: A:R.119, A:N.146, A:N.146, A:Q.153 GOL.5: 6 residues within 4Å: Chain A: F.4, L.5, S.120, L.121 Chain B: R.117, L.121 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.5, A:S.120, B:R.117 Water bridges: A:L.121, A:L.121 GOL.6: 4 residues within 4Å: Chain A: T.60, Y.64, N.72, R.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.64, A:N.72, A:R.84 GOL.7: 4 residues within 4Å: Chain A: V.89, Y.90, R.91, E.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.91 GOL.8: 4 residues within 4Å: Chain A: D.173, E.175, D.176, Q.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.175, A:D.176, A:Q.177 GOL.9: 9 residues within 4Å: Chain A: D.20, K.24, W.110, A.124, F.125, R.127, D.128 Chain B: A.124, R.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.20, A:D.20, A:K.24, A:A.124 GOL.13: 7 residues within 4Å: Chain B: T.60, Y.64, N.72, K.74, F.75, I.76 Ligands: GNP.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.74, B:I.76 Water bridges: B:I.76 GOL.14: 6 residues within 4Å: Chain B: D.54, R.119, N.146, N.149, W.150, Q.153 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.119, B:R.119, B:N.146, B:N.149

2 x 05Y: ~{N}-[1-(2-pyridin-2-ylethyl)benzimidazol-2-yl]propanamide(Covalent)

05Y.10: 10 residues within 4Å: Chain A: K.48, R.127, D.128, A.129, M.130, Y.159, C.160, I.218, R.221, M.222 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.221, A:M.222 Hydrogen bonds: A:R.221 05Y.15: 10 residues within 4Å: Chain B: K.48, R.127, D.128, A.129, M.130, Y.159, C.160, I.218, R.221, M.222 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.130, B:Y.159, B:I.218, B:M.222 pi-Stacking: B:Y.159

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
B

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