SMTL ID : 9gvu.1

Human Rab27A in complex with cyclic peptide IMP-2660

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.19, T.37, D.70 Ligands: GNP.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.19, A:T.37, H2O.1, H2O.1 MG.10: 4 residues within 4Å: Chain B: T.19, T.37, D.70 Ligands: GNP.16 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.19, B:T.37, H2O.4, H2O.5

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: N.31, K.33, F.34, I.35 Ligands: GNP.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.33, A:I.35, A:I.35 Water bridges: A:N.31 GOL.3: 3 residues within 4Å: Chain A: S.32, L.133 Ligands: GNP.9 No protein-ligand interaction detected (PLIP) GOL.4: 5 residues within 4Å: Chain A: D.132, L.133, E.134, D.135, Q.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.134, A:D.135, A:Q.136 GOL.5: 3 residues within 4Å: Chain A: R.137, V.138, V.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.137, A:V.138 Water bridges: A:R.137 GOL.6: 4 residues within 4Å: Chain A: R.50, G.59, R.60, G.61 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.50, A:R.50, A:G.59, A:G.61 GOL.7: 2 residues within 4Å: Chain A: V.48, R.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.50, A:R.50 GOL.8: 4 residues within 4Å: Chain A: R.180, E.182 Chain D: L.1, V.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.180, A:E.182, A:E.182, D:V.2, D:V.2 Water bridges: A:S.119 GOL.11: 5 residues within 4Å: Chain B: D.132, L.133, E.134, D.135, Q.136 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.135, B:Q.136 GOL.12: 3 residues within 4Å: Chain B: S.32, L.133 Ligands: GNP.16 No protein-ligand interaction detected (PLIP) GOL.13: 6 residues within 4Å: Chain B: T.19, N.31, K.33, F.34, I.35 Ligands: GNP.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.35, B:I.35 GOL.14: 3 residues within 4Å: Chain B: I.153, P.154, Y.155 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.155 GOL.15: 4 residues within 4Å: Chain A: T.82 Chain B: F.42, R.43, E.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.44 Water bridges: B:F.42 GOL.17: 3 residues within 4Å: Chain C: V.2, G.3, S.4 No protein-ligand interaction detected (PLIP) GOL.18: 7 residues within 4Å: Chain A: R.86 Chain B: Y.2 Chain C: N.11, X.12 Chain D: R.5, H.6, T.7 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:N.11, D:R.5, D:T.7, A:R.86

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

GNP.9: 26 residues within 4Å: Chain A: D.13, S.14, G.15, V.16, G.17, K.18, T.19, S.20, F.30, N.31, S.32, K.33, F.34, T.36, T.37, G.73, N.129, K.130, D.132, L.133, S.159, A.160, A.161 Ligands: MG.1, GOL.2, GOL.3 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:G.15, A:V.16, A:G.17, A:K.18, A:K.18, A:K.18, A:T.19, A:S.20, A:S.20, A:N.31, A:T.37, A:T.71, A:G.73, A:N.129, A:K.130, A:K.130, A:A.160, A:A.161 Water bridges: A:T.19, A:T.37, A:T.37, A:L.74, A:L.74 Salt bridges: A:D.132 pi-Stacking: A:F.30, A:F.30 pi-Cation interactions: A:K.130 GNP.16: 27 residues within 4Å: Chain B: D.13, S.14, G.15, V.16, G.17, K.18, T.19, S.20, F.30, N.31, S.32, K.33, F.34, T.36, T.37, T.71, G.73, N.129, K.130, D.132, L.133, S.159, A.160, A.161 Ligands: MG.10, GOL.12, GOL.13 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:G.15, B:V.16, B:G.17, B:K.18, B:K.18, B:K.18, B:T.19, B:T.19, B:S.20, B:S.20, B:N.31, B:T.36, B:T.37, B:T.37, B:T.71, B:G.73, B:N.129, B:K.130, B:K.130, B:A.160, B:A.161 Salt bridges: B:D.132 pi-Stacking: B:F.30, B:F.30 pi-Cation interactions: B:K.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petracca, R. et al., A potent macrocyclic peptide modulator of Rab27a identified by RaPID screening. To Be Published

Release Date

2025-10-15

Peptides

Ras-related protein Rab-27A: AB
Cyclic peptide IMP-2660: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
F

Ras-related protein Rab-27A

Cyclic peptide IMP-2660