SMTL ID : 2p2l.1 (1 other biounit)

Rac1-GDP-Zinc Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: T.21, T.39, D.61 Ligands: GDP.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.21, A:T.39, H2O.1, H2O.9, H2O.10 ZN.2: 3 residues within 4Å: Chain A: D.67, E.104, H.108 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.67, A:D.67, A:E.104, A:E.104, A:H.108 ZN.3: 3 residues within 4Å: Chain A: D.42 Chain B: D.42 Chain C: D.42 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C Metal complexes: B:D.42, A:D.42, A:D.42, C:D.42, C:D.42 ZN.4: 2 residues within 4Å: Chain A: E.131, E.135 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.131, A:E.135 ZN.6: 4 residues within 4Å: Chain B: T.21, T.39, D.61 Ligands: GDP.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.21, B:T.39, H2O.19, H2O.19, H2O.20 ZN.7: 3 residues within 4Å: Chain B: D.67, E.104, H.108 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.67, B:D.67, B:E.104, B:E.104, B:H.108 ZN.9: 3 residues within 4Å: Chain C: T.21, T.39 Ligands: GDP.11 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.21, C:T.39, H2O.30, H2O.30, H2O.30 ZN.10: 3 residues within 4Å: Chain C: D.67, E.104, H.108 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.67, C:D.67, C:E.104, C:E.104, C:H.108

3 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.5: 17 residues within 4Å: Chain A: D.15, G.16, A.17, V.18, G.19, K.20, T.21, C.22, F.32, I.37, K.120, D.122, L.123, S.162, A.163, L.164 Ligands: ZN.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:D.15, A:A.17, A:V.18, A:G.19, A:K.20, A:T.21, A:C.22, A:K.120, A:K.120, A:A.163, A:L.164 Water bridges: A:K.20, A:T.21, A:L.23 Salt bridges: A:K.20, A:D.122 pi-Stacking: A:F.32, A:F.32 GDP.8: 18 residues within 4Å: Chain A: N.47 Chain B: D.15, G.16, A.17, V.18, G.19, K.20, T.21, C.22, F.32, I.37, K.120, D.122, L.123, S.162, A.163, L.164 Ligands: ZN.6 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.15, B:A.17, B:V.18, B:G.19, B:K.20, B:T.21, B:C.22, B:K.120, B:K.120, B:A.163, B:L.164, A:N.47 Water bridges: B:K.20, B:T.21, B:L.23 Salt bridges: B:K.20, B:D.122 pi-Stacking: B:F.32, B:F.32 GDP.11: 18 residues within 4Å: Chain B: N.47 Chain C: D.15, G.16, A.17, V.18, G.19, K.20, T.21, C.22, F.32, I.37, K.120, D.122, L.123, S.162, A.163, L.164 Ligands: ZN.9 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.15, C:A.17, C:V.18, C:G.19, C:K.20, C:T.21, C:C.22, C:K.120, C:A.163, C:L.164, B:N.47 Water bridges: C:K.20, C:T.21, C:L.23, C:K.120, C:K.120, C:K.120 Salt bridges: C:K.20, C:D.122 pi-Stacking: C:F.32, C:F.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prehna, G. et al., A Rac1-GDP trimer complex binds zinc with tetrahedral and octahedral coordination, displacing magnesium. Acta Crystallogr.,Sect.D (2007)

Release Date

2007-05-01

Peptides

Ras-related C3 botulinum toxin substrate 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ras-related C3 botulinum toxin substrate 1

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