SMTL ID : 2w83.1

Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

hetero-3-2-mer

Ligands

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

GTP.1: 21 residues within 4Å: Chain A: L.11, D.12, A.13, A.14, G.15, K.16, T.17, T.18, T.31, P.33, T.34, G.55, G.56, N.112, K.113, D.115, L.116, C.145, A.146, T.147 Ligands: MG.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:A.13, A:A.14, A:G.15, A:K.16, A:T.17, A:T.18, A:T.18, A:T.31, A:T.34, A:T.34, A:G.56, A:N.112, A:K.113, A:K.113, A:A.146, A:T.147 Water bridges: A:T.17, A:T.18, A:V.29, A:T.31, A:T.31, A:T.31, A:T.34, A:L.57, A:L.57 Salt bridges: A:K.16, A:K.16, A:D.115 GTP.5: 21 residues within 4Å: Chain B: L.11, D.12, A.13, A.14, G.15, K.16, T.17, T.18, T.31, P.33, T.34, G.55, G.56, N.112, K.113, D.115, L.116, C.145, A.146, T.147 Ligands: MG.6 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:A.13, B:A.14, B:G.15, B:K.16, B:T.17, B:T.18, B:T.18, B:T.34, B:G.56, B:N.112, B:K.113, B:K.113, B:A.146, B:T.147 Water bridges: B:K.16, B:T.17, B:T.17, B:T.34 Salt bridges: B:K.16, B:K.16, B:D.115 GTP.9: 21 residues within 4Å: Chain E: L.11, D.12, A.13, A.14, G.15, K.16, T.17, T.18, T.31, P.33, T.34, G.55, G.56, N.112, K.113, D.115, L.116, C.145, A.146, T.147 Ligands: MG.10 27 PLIP interactions: 27 interactions with chain E Hydrogen bonds: E:A.13, E:A.14, E:G.15, E:K.16, E:T.17, E:T.18, E:T.18, E:T.34, E:G.56, E:N.112, E:K.113, E:K.113, E:A.146, E:T.147 Water bridges: E:T.17, E:T.17, E:T.18, E:T.31, E:T.31, E:T.31, E:T.34, E:T.34, E:L.57, E:L.57 Salt bridges: E:K.16, E:K.16, E:D.115

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.17, T.34 Ligands: GTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.17, A:T.34, H2O.2, H2O.4 MG.6: 3 residues within 4Å: Chain B: T.17, T.34 Ligands: GTP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.17, B:T.34, H2O.5, H2O.5 MG.10: 3 residues within 4Å: Chain E: T.17, T.34 Ligands: GTP.9 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.17, E:T.34, H2O.9, H2O.11

6 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.3: 8 residues within 4Å: Chain A: P.122, H.123, Q.126, W.139, V.141 Chain E: P.122, Q.126, V.141 No protein-ligand interaction detected (PLIP) DIO.7: 4 residues within 4Å: Chain A: I.60, L.63 Chain C: I.30 Ligands: DIO.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.36 DIO.8: 8 residues within 4Å: Chain A: K.59, P.62, L.63 Chain C: E.23, N.26, A.27, I.30 Ligands: DIO.7 No protein-ligand interaction detected (PLIP) DIO.11: 6 residues within 4Å: Chain A: K.121, P.122, H.123 Chain E: K.121, P.122, H.123 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:H.123, A:H.123 DIO.12: 2 residues within 4Å: Chain E: K.24, L.25 No protein-ligand interaction detected (PLIP) DIO.13: 4 residues within 4Å: Chain E: K.59, I.60, P.62, L.63 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: R.61, P.62, W.64, R.65, Y.68, E.92, R.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.65, A:R.65, A:R.95 Water bridges: A:R.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Isabet, T. et al., The Structural Basis of Arf Effector Specificity: The Crystal Structure of Arf6 in a Complex with Jip4. Embo J. (2009)

Release Date

2009-07-14

Peptides

ADP-RIBOSYLATION FACTOR 6: ABE
C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

C
C

D
D

ADP-RIBOSYLATION FACTOR 6

C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4