SMTL ID : 6s5h.1

Structure of the human RAB38 in complex with GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 24 residues within 4Å: Chain A: D.18, L.19, G.20, V.21, G.22, K.23, T.24, S.25, F.35, S.36, S.37, Y.39, A.41, T.42, A.68, G.69, N.128, K.129, D.131, Q.132, S.160, A.161, K.162 Ligands: MG.11 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.20, A:V.21, A:G.22, A:K.23, A:T.24, A:S.25, A:S.25, A:S.36, A:T.42, A:G.69, A:N.128, A:K.129, A:K.129, A:S.160, A:A.161, A:K.162 Water bridges: A:T.24, A:T.42, A:D.66 Salt bridges: A:K.23, A:K.23, A:D.131 pi-Stacking: A:F.35, A:F.35

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: M.76, Y.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.80 EDO.3: 4 residues within 4Å: Chain A: N.34, F.35, S.36, R.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.34, A:F.35, A:R.40 EDO.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: L.19, G.20, R.95 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.20, A:G.20, A:R.95 EDO.6: 1 residues within 4Å: Chain A: F.47 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain A: Y.30, V.31, Q.33, L.49, K.50, V.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.31, A:Q.33, A:V.51 EDO.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: V.93, A.127, N.140, M.144, E.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.140 EDO.10: 3 residues within 4Å: Chain A: F.99, E.100, A.103 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.100, A:H.151

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 4 residues within 4Å: Chain A: T.24, T.42, D.66 Ligands: GTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.42, H2O.1, H2O.2

3 x BR: BROMIDE ION(Non-covalent)

BR.12: 1 residues within 4Å: Chain A: Q.70 Ligand excluded by PLIP BR.13: 1 residues within 4Å: Chain A: A.97 Ligand excluded by PLIP BR.14: 1 residues within 4Å: Chain A: H.38 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Saez, L. et al., Structure of the human RAB38 in complex with GTP. To Be Published

Release Date

2020-07-22

Peptides

Ras-related protein Rab-38: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ras-related protein Rab-38