SMTL ID : 9ikq.1

Crystal structure of OPTN LZD in complex with GTP-bound Rab8a(Q67L)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

hetero-2-2-mer

Ligands

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

GTP.1: 24 residues within 4Å: Chain A: D.16, S.17, G.18, V.19, G.20, K.21, T.22, C.23, F.33, S.35, T.36, F.37, S.39, T.40, A.65, G.66, N.121, K.122, D.124, V.125, S.151, A.152, K.153 Ligands: MG.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:G.18, A:V.19, A:G.20, A:K.21, A:T.22, A:C.23, A:S.35, A:S.39, A:T.40, A:T.40, A:T.64, A:G.66, A:N.121, A:K.122, A:K.122, A:S.151, A:A.152, A:K.153 Water bridges: A:T.22, A:I.38, A:L.67, A:K.153, A:K.153 Salt bridges: A:K.21, A:K.21, A:D.124 pi-Stacking: A:F.33, A:F.33 GTP.8: 25 residues within 4Å: Chain D: D.16, S.17, G.18, V.19, G.20, K.21, T.22, C.23, F.33, N.34, S.35, F.37, S.39, T.40, A.65, G.66, N.121, K.122, D.124, V.125, S.151, A.152, K.153 Ligands: GOL.11, MG.13 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:G.18, D:V.19, D:G.20, D:K.21, D:T.22, D:C.23, D:N.34, D:T.40, D:T.64, D:G.66, D:N.121, D:K.122, D:K.122, D:S.151, D:A.152, D:K.153 Water bridges: D:S.17, D:T.22, D:T.40, D:D.63, D:L.67 Salt bridges: D:K.21, D:K.21, D:D.124 pi-Stacking: D:F.33, D:F.33

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.22, T.40, D.63 Ligands: GTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.22, A:T.40, H2O.1, H2O.1 MG.13: 4 residues within 4Å: Chain D: T.22, T.40, D.63 Ligands: GTP.8 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.22, D:T.40, H2O.10, H2O.11

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

EDO.3: 5 residues within 4Å: Chain A: A.112, K.116, Y.143, G.144, I.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.112, A:K.116, A:G.144 EDO.4: 7 residues within 4Å: Chain A: R.27, F.28, D.31, R.48, N.155, V.158, E.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.48, A:N.155 EDO.5: 5 residues within 4Å: Chain A: G.66, L.67, E.68, R.71, W.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.74, A:T.74 EDO.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.7: 1 residues within 4Å: Chain A: L.141 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain D: T.22, F.26, K.46 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.46 Water bridges: D:T.22

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain B: Q.33 Chain C: I.28 Chain D: K.10, W.62, Y.77 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.33, D:K.10 GOL.11: 4 residues within 4Å: Chain D: T.91, K.122, V.125 Ligands: GTP.8 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.91, D:K.122 Water bridges: D:T.91 GOL.12: 6 residues within 4Å: Chain D: E.68, R.71, N.98, N.101, W.102, N.105 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.71, D:N.98, D:N.101, D:N.105 Water bridges: D:E.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Molecular Basis of the Recognition of the Active Rab8a by Optineurin. J.Mol.Biol. (2024)

Release Date

2024-12-25

Peptides

Ras-related protein Rab-8A: AD
Optineurin: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

B
C

C
D

Ras-related protein Rab-8A

Optineurin