SMTL ID : 8p3k.1

Fusion hSlp2-a_Rab27A non-covalent complex with compound IMP-2505

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

homo-dimer

Ligands

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

GNP.1: 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, T.78, T.79, A.114, G.115, N.171, K.172, D.174, L.175, S.201, A.202, A.203 Ligands: GOL.4, GOL.5, GOL.6, MG.7 24 PLIP interactions: 24 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:K.60, A:T.61, A:S.62, A:S.62, A:N.73, A:T.78, A:T.78, A:T.78, A:T.79, A:T.79, A:N.171, A:K.172, A:A.202, A:A.203 Salt bridges: A:D.174 pi-Stacking: A:F.72, A:F.72 pi-Cation interactions: A:K.172 GNP.9: 28 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, F.76, I.77, T.78, T.79, T.113, A.114, G.115, L.116, N.171, K.172, D.174, L.175, S.201, A.202, A.203 Ligands: GOL.12, MG.16 22 PLIP interactions: 22 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:G.115, B:N.171, B:K.172, B:S.201, B:A.202, B:A.203 Salt bridges: B:D.174 pi-Stacking: B:F.72, B:F.72

2 x WTB: (2~{S})-~{N}-(3-methoxyphenyl)-1-[4-(prop-2-enoylamino)phenyl]sulfonyl-pyrrolidine-2-carboxamide(Non-covalent)

WTB.2: 8 residues within 4Å: Chain A: N.163, P.164, D.165, I.166, I.195, P.196, L.218, R.222 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.218 Hydrogen bonds: A:P.164, A:I.166 WTB.8: 15 residues within 4Å: Chain B: K.25, E.28, K.49, R.128, D.129, A.130, M.131, G.132, F.133, A.159, Y.160, N.163, P.164, D.165, R.222 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:M.131, B:F.133, B:A.159, B:Y.160, B:P.164 Hydrogen bonds: B:K.49, B:D.165

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: T.61, Y.65, D.83, R.85 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.83, A:R.85 GOL.4: 4 residues within 4Å: Chain A: S.74, K.75, F.76 Ligands: GNP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.76 GOL.5: 9 residues within 4Å: Chain A: T.61, S.62, Y.65, N.73, K.75, F.76, I.77 Ligands: GNP.1, GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.62, A:I.77, A:I.77 Water bridges: A:N.73 GOL.6: 2 residues within 4Å: Chain A: S.74 Ligands: GNP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.74 GOL.10: 3 residues within 4Å: Chain B: P.196, Y.197, M.214 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.197 GOL.11: 7 residues within 4Å: Chain B: N.163, P.164, D.165, I.166, G.194, I.195 Ligands: GOL.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.163, B:P.164, B:D.165, B:D.165, B:I.166 GOL.12: 8 residues within 4Å: Chain B: T.61, S.62, Y.65, N.73, K.75, F.76, I.77 Ligands: GNP.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.75, B:I.77 GOL.13: 6 residues within 4Å: Chain B: S.173, D.174, E.176, S.201, N.204, T.206 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.173, B:N.204, B:N.204 GOL.14: 2 residues within 4Å: Chain B: R.149, K.192 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.149 GOL.15: 7 residues within 4Å: Chain B: Q.156, N.163, P.164, I.166, Y.193, I.195 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.156, B:N.163, B:Y.193

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 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.16: 3 residues within 4Å: Chain B: T.61, T.79 Ligands: GNP.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.61, B:T.79, H2O.2, H2O.2

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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