SMTL ID : 1r8q.3 (5 other biounits)

FULL-LENGTH ARF1-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SEC7 DOMAIN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.31, E.54 Ligands: G3D.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.31, H2O.1, H2O.2, H2O.4, H2O.5 MG.5: 3 residues within 4Å: Chain C: T.31, E.54 Ligands: G3D.6 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.31, H2O.8, H2O.10, H2O.10, H2O.10

2 x G3D: GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE(Non-covalent)

G3D.2: 16 residues within 4Å: Chain A: L.25, D.26, A.27, A.28, G.29, K.30, T.31, T.32, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:A.27, A:A.28, A:G.29, A:K.30, A:T.31, A:T.31, A:T.32, A:T.32, A:N.126, A:K.127, A:K.127, A:A.160, A:T.161 Water bridges: A:T.31 Salt bridges: A:K.30, A:D.129 pi-Cation interactions: A:K.127 G3D.6: 16 residues within 4Å: Chain C: L.25, D.26, A.27, A.28, G.29, K.30, T.31, T.32, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Ligands: MG.5 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:A.27, C:A.28, C:G.29, C:K.30, C:T.31, C:T.31, C:T.32, C:T.32, C:N.126, C:K.127, C:K.127, C:A.160, C:T.161 Water bridges: C:G.24, C:K.30, C:T.31, C:T.31, C:T.31, C:E.54 Salt bridges: C:K.30, C:D.129

2 x AFB: 1,6,7,8,9,11A,12,13,14,14A-DECAHYDRO-1,13-DIHYDROXY-6-METHYL-4H-CYCLOPENT[F]OXACYCLOTRIDECIN-4-ONE(Non-covalent)

AFB.3: 14 residues within 4Å: Chain A: F.51, V.53, T.64, V.65, W.66, D.67, I.74, W.78, Y.81 Chain B: A.108, Y.141, M.145, T.148, V.155 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:A.108, B:T.148, A:F.51, A:F.51, A:W.66, A:W.66, A:W.66 Hydrogen bonds: B:Y.141, A:D.67, A:D.67, A:W.78 Water bridges: A:V.65 AFB.7: 13 residues within 4Å: Chain C: F.51, V.53, T.64, V.65, W.66, D.67, I.74, W.78, Y.81 Chain D: Y.141, M.145, T.148, V.155 11 PLIP interactions: 2 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:T.148, C:F.51, C:F.51, C:F.51, C:W.66, C:W.66, C:W.66 Hydrogen bonds: D:Y.141, C:D.67, C:D.67, C:W.78

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain B: H.78, D.82 Chain D: H.78, D.82 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:H.78, D:D.82, B:H.78, B:D.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Renault, L. et al., Structural snapshots of the mechanism and inhibition of a guanine nucleotide exchange factor. Nature (2003)

Release Date

2004-01-20

Peptides

ADP-ribosylation factor 1: AC
Arno: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
E

D
F

ADP-ribosylation factor 1

Arno

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