SMTL ID : 8p3j.1

Fusion hSlp2-a_Rab27A non-covalent complex with hit fragment IMP-1704

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

4 x WT6: ~{N}-(4-pyrrolidin-1-ylsulfonylphenyl)prop-2-enamide(Covalent)(Non-covalent)

WT6.1: 8 residues within 4Å: Chain A: K.49, R.128, D.129, A.130, M.131, D.165, I.219, R.222 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.131, A:R.222, A:R.222 Hydrogen bonds: A:K.49, A:D.129 WT6.2: 9 residues within 4Å: Chain A: N.163, P.164, D.165, I.166, G.194, I.195, P.196, L.218, R.225 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.163, A:I.195, A:L.218 WT6.6: 5 residues within 4Å: Chain B: K.49, R.128, A.130, M.131, A.161 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.161 Hydrogen bonds: B:K.49, B:A.130 WT6.8: 9 residues within 4Å: Chain B: E.162, N.163, P.164, D.165, I.166, G.194, I.195, P.196, R.222 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.163, B:I.195 Hydrogen bonds: B:I.166, B:G.194, B:R.225

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

GNP.3: 26 residues within 4Å: Chain A: S.56, G.57, V.58, G.59, K.60, T.61, S.62, F.72, N.73, S.74, F.76, I.77, T.78, T.79, T.113, A.114, G.115, N.171, K.172, D.174, L.175, S.201, A.202, A.203 Ligands: GOL.4, MG.5 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.57, A:V.58, A:G.59, A:K.60, A:K.60, A:K.60, A:T.61, A:S.62, A:S.62, A:N.73, A:T.78, 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:I.77, A:I.77 Salt bridges: A:D.174 pi-Stacking: A:F.72, A:F.72 pi-Cation interactions: A:K.172 GNP.7: 25 residues within 4Å: Chain B: S.56, G.57, V.58, G.59, K.60, T.61, S.62, F.72, N.73, S.74, F.76, I.77, T.78, T.79, T.113, A.114, G.115, N.171, K.172, D.174, L.175, S.201, A.202, A.203 Ligands: MG.11 23 PLIP interactions: 23 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:K.60, B:T.61, B:T.61, B:S.62, B:S.62, B:N.73, B:T.79, B:T.113, B:G.115, B:N.171, B:K.172, B:K.172, B:A.202, B:A.203 Salt bridges: B:D.174 pi-Stacking: B:F.72, B:F.72

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: S.74, L.175 Ligands: GNP.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.74 GOL.9: 5 residues within 4Å: Chain B: D.174, L.175, E.176, D.177, Q.178 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.176, B:D.177, B:Q.178 GOL.10: 3 residues within 4Å: Chain B: L.116, E.117, R.118 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.118, B:R.118, B:R.118

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: T.61, T.79, D.112 Ligands: GNP.3 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.11: 3 residues within 4Å: Chain B: T.61, T.79 Ligands: GNP.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.61, B:T.79, H2O.3, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Vita, E. et al., Targeted covalent inhibitors of the small GTPase Rab27A. To Be Published

Release Date

2024-11-20

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

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