SMTL ID : 5bwm.1

The complex structure of C3cer exoenzyme and GDP bound RhoA (NADH-bound state)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

GDP.1: 17 residues within 4Å: Chain A: D.13, G.14, A.15, C.16, G.17, K.18, T.19, C.20, F.30, V.35, K.118, D.120, L.121, S.160, A.161, K.162 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:D.13, A:A.15, A:C.16, A:G.17, A:K.18, A:T.19, A:C.20, A:K.118, A:K.118, A:A.161, A:K.162 Water bridges: A:T.19, A:T.19 Salt bridges: A:K.18, A:D.120 pi-Stacking: A:F.30

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.19, T.37 Ligands: GDP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.19, A:T.37, H2O.1, H2O.1

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 22 residues within 4Å: Chain A: E.40, N.41 Chain B: T.48, A.51, N.55, R.59, R.97, G.98, D.99, D.100, W.102, I.103, E.137, S.142, T.143, G.150, Y.151, A.152, R.155, Q.183, E.185 Ligands: EDO.4 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.151 Hydrogen bonds: B:N.55, B:R.97, B:G.98, B:G.98, B:D.99, B:D.100, B:D.100, B:E.137, B:Y.151, B:A.152, B:R.155, B:E.185, A:N.41 Salt bridges: B:R.59, B:R.97, B:R.97, B:R.155

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain B: R.59, R.97, E.137, Y.194 Ligands: NAI.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.59, B:R.97, B:R.97, B:Y.194 EDO.5: 9 residues within 4Å: Chain B: M.172, N.173, T.178, Y.180, P.181, G.182, Q.183, Y.184, E.185 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.173, B:T.178, B:G.182, B:Q.183, B:Q.183, B:Y.184, B:E.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toda, A. et al., Rho GTPase Recognition by C3 Exoenzyme Based on C3-RhoA Complex Structure. J.Biol.Chem. (2015)

Release Date

2015-06-24

Peptides

Transforming protein RhoA: A
ADP-ribosyltransferase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transforming protein RhoA

ADP-ribosyltransferase

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