SMTL ID : 7opq.1

Rab27a fusion with Slp2a-RBDa1 effector covalent adduct with CA1 in C188

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

2 x 06D: 1-[(2~{S})-2-(4-methoxyphenyl)pyrrolidin-1-yl]propan-1-one(Covalent)

06D.1: 8 residues within 4Å: Chain A: K.48, A.129, M.130, Y.159, I.218, R.221, M.222, C.225 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.159, A:I.218, A:M.222 pi-Stacking: A:Y.159 06D.10: 8 residues within 4Å: Chain B: K.48, A.129, M.130, Y.159, I.218, R.221, M.222, C.225 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.159, B:M.222 pi-Stacking: B:Y.159

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

GNP.2: 25 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.3, GOL.7 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:S.55, 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:T.60, A:T.77 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.14 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:I.76, 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:T.78, B:T.78, B:L.115 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.3: 4 residues within 4Å: Chain A: T.60, T.78, D.111 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.60, A:T.78, H2O.1, H2O.1 MG.12: 3 residues within 4Å: Chain B: T.60, T.78 Ligands: GNP.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.60, B:T.78, H2O.5, H2O.5

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: S.172, D.173, S.200, N.203, T.205 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.172, A:N.203, A:T.205 GOL.5: 5 residues within 4Å: Chain A: D.173, L.174, 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.6: 6 residues within 4Å: Chain A: D.54, R.119, N.146, N.149, W.150, Q.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.54, A:R.119, A:N.149 Water bridges: A:Q.153, A:Q.153 GOL.7: 8 residues within 4Å: Chain A: T.60, S.61, Y.64, N.72, K.74, F.75, I.76 Ligands: GNP.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.74, A:I.76 GOL.8: 5 residues within 4Å: Chain A: F.4, L.5, S.120 Chain B: R.117, L.121 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:L.121 Hydrogen bonds: B:R.117 GOL.9: 6 residues within 4Å: Chain A: Q.155, E.161, N.162, P.163, I.165, Y.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.155, A:N.162, A:P.163, A:Y.192 GOL.13: 5 residues within 4Å: Chain B: D.54, R.119, N.146, N.149, W.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.54, B:R.119 Water bridges: B:R.119 GOL.14: 7 residues within 4Å: Chain B: T.60, S.61, N.72, K.74, F.75, I.76 Ligands: GNP.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.74, B:I.76

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