SMTL ID : 5lef.1

Rab6A:Kif20A complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

hetero-2-2-mer

Ligands

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

GTP.1: 24 residues within 4Å: Chain A: Q.18, S.19, V.20, G.21, K.22, T.23, S.24, F.34, D.35, N.36, Y.38, Q.39, A.40, T.41, A.66, G.67, N.122, K.123, D.125, L.126, S.152, A.153, K.154 Ligands: MG.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:S.19, A:V.20, A:G.21, A:K.22, A:T.23, A:S.24, A:S.24, A:N.36, A:Y.38, A:Q.39, A:T.41, A:G.67, A:N.122, A:K.123, A:K.123, A:S.152, A:A.153, A:K.154 Water bridges: A:S.19, A:L.68, A:K.154, A:K.154 Salt bridges: A:K.22, A:K.22, A:D.125 pi-Stacking: A:F.34, A:F.34 GTP.5: 27 residues within 4Å: Chain B: E.17, Q.18, S.19, V.20, G.21, K.22, T.23, S.24, F.34, D.35, N.36, T.37, Y.38, Q.39, A.40, T.41, A.66, G.67, N.122, K.123, D.125, L.126, S.152, A.153, K.154 Ligands: MG.6, IPA.9 32 PLIP interactions: 32 interactions with chain B Hydrogen bonds: B:S.19, B:V.20, B:G.21, B:K.22, B:T.23, B:T.23, B:S.24, B:S.24, B:N.36, B:Y.38, B:T.41, B:G.67, B:N.122, B:K.123, B:K.123, B:S.152, B:A.153, B:K.154 Water bridges: B:T.23, B:N.36, B:N.36, B:Y.38, B:T.41, B:T.41, B:L.68, B:K.154, B:K.154 Salt bridges: B:K.22, B:K.22, B:D.125 pi-Stacking: B:F.34, B:F.34

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.22, T.23, T.41, D.64 Ligands: GTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.23, A:T.41, H2O.1, H2O.2 MG.6: 5 residues within 4Å: Chain B: K.22, T.23, T.41, D.64 Ligands: GTP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.23, B:T.41, H2O.7, H2O.7

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: R.28, D.32, S.33, F.34 3 PLIP interactions: 3 interactions with chain A Water bridges: A:F.34, A:F.34 Salt bridges: A:R.28 SO4.7: 4 residues within 4Å: Chain B: R.28, D.32, S.33, F.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.34 Salt bridges: B:R.28 SO4.8: 6 residues within 4Å: Chain B: G.156, Y.157, N.158, V.159, K.160, Q.161 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.156, B:N.158, B:V.159, B:K.160, B:Q.161, B:Q.161

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: E.138, F.148, I.149, R.165 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.148, A:R.165, A:R.165 Water bridges: A:F.148

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.9: 7 residues within 4Å: Chain B: T.23, S.24, D.35, T.37, Y.38, Q.39 Ligands: GTP.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.23 Hydrogen bonds: B:Q.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miserey-Lenkei, S. et al., Coupling fission and exit of RAB6 vesicles at Golgi hotspots through kinesin-myosin interactions. Nat Commun (2017)

Release Date

2017-11-15

Peptides

Ras-related protein Rab-6A: AB
Kinesin-like protein KIF20A: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ras-related protein Rab-6A

Kinesin-like protein KIF20A