SMTL ID : 4kax.1

Crystal structure of the Grp1 PH domain in complex with Arf6-GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-mer

Ligands

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

GTP.1: 21 residues within 4Å: Chain A: L.16, D.17, A.18, A.19, G.20, K.21, T.22, T.23, T.36, P.38, T.39, G.60, G.61, N.117, K.118, D.120, L.121, C.150, A.151, T.152 Ligands: MG.2 32 PLIP interactions: 32 interactions with chain A Hydrogen bonds: A:A.18, A:A.19, A:G.20, A:K.21, A:T.22, A:T.22, A:T.23, A:T.23, A:T.36, A:T.39, A:T.39, A:G.61, A:N.117, A:K.118, A:K.118, A:A.151, A:T.152 Water bridges: A:K.21, A:T.23, A:T.36, A:T.36, A:T.36, A:T.36, A:T.36, A:T.39, A:L.62, A:L.62, A:T.152, A:T.152 Salt bridges: A:K.21, A:K.21, A:D.120

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.22, T.39 Ligands: GTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.22, A:T.39, H2O.3, H2O.3

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 1 residues within 4Å: Chain A: K.50 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.50 Salt bridges: A:K.50, A:K.50

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: L.28, K.29, T.46, V.47, T.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.29, A:T.48 GOL.7: 5 residues within 4Å: Chain B: L.36, W.43, D.82, R.84, R.121 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.82, B:R.121 Water bridges: B:W.43, B:R.84, B:R.121 GOL.8: 6 residues within 4Å: Chain A: K.64 Chain B: F.25, N.26, D.28, T.51, D.52 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.26, B:D.28, B:T.51, B:D.52, A:K.64 Water bridges: B:D.52, B:D.52, B:N.53, A:K.64 GOL.9: 7 residues within 4Å: Chain B: T.21, F.24, W.47, I.49, F.58, T.61, D.63 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.47, B:D.63 Water bridges: B:T.21, B:T.21, B:F.24

1 x K: POTASSIUM ION(Non-covalent)

K.5: 3 residues within 4Å: Chain A: H.71, T.74 Chain B: G.110 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:G.110, A:H.71, A:T.74, H2O.3, H2O.11

1 x 4IP: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE(Non-covalent)

4IP.6: 13 residues within 4Å: Chain B: K.35, G.37, G.38, R.39, V.40, T.42, K.44, R.46, Y.57, R.67, K.105, N.116, H.117 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:G.38, B:R.39, B:V.40, B:T.42, B:T.42, B:T.42, B:Y.57, B:N.116 Water bridges: B:K.35, B:K.44, B:R.67, B:K.105, B:K.105 Salt bridges: B:K.35, B:K.35, B:K.44, B:R.46, B:R.67, B:K.105, B:K.105, B:H.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malaby, A.W. et al., Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-08-14

Peptides

ADP-ribosylation factor 6: A
Cytohesin-3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-ribosylation factor 6

Cytohesin-3