SMTL ID : 5vys.1

Crystal structure of the WbkC N-formyltransferase (C47S variant) from Brucella melitensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 1YJ: N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid(Non-covalent)

1YJ.1: 12 residues within 4Å: Chain A: Y.89, S.91, L.92, I.93, L.98, N.107, H.138, M.140, D.141, N.143, F.144, D.145 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.93, A:I.93, A:D.141, A:D.145 Water bridges: A:T.146, A:T.146 1YJ.4: 11 residues within 4Å: Chain B: S.91, L.92, I.93, L.98, N.107, H.138, M.140, D.141, N.143, F.144, D.145 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:I.93, B:I.93, B:D.141, B:D.145 Water bridges: B:D.141, B:T.146 pi-Stacking: B:F.144

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

EDO.2: 6 residues within 4Å: Chain A: E.130, V.157, E.158, E.159, R.222, R.225 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.158, A:R.222, A:R.222, A:R.225, A:R.225

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

GDP.3: 14 residues within 4Å: Chain A: R.47, R.90, T.119, N.120, V.122, A.123, A.163, F.167, R.203, L.205, M.227, F.229, F.232, P.233 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.120, A:R.203, A:P.233 Water bridges: A:R.90, A:R.90, A:S.121, A:S.121, A:F.229 Salt bridges: A:R.47, A:R.90, A:R.90 pi-Stacking: A:F.232, A:F.232 GDP.5: 12 residues within 4Å: Chain B: R.47, R.90, T.119, N.120, A.123, A.163, F.167, L.205, M.227, F.229, F.232, P.233 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.120, B:M.227 Water bridges: B:R.90, B:R.90, B:R.90, B:R.90, B:S.121, B:S.121 Salt bridges: B:R.47, B:R.90 pi-Stacking: B:F.232, B:F.232

1 x GMP: GUANOSINE(Non-covalent)

GMP.6: 8 residues within 4Å: Chain B: R.90, S.91, H.109, G.118, T.119, F.144, D.145, R.203 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:L.92, B:H.109, B:G.118 Water bridges: B:R.90, B:R.90, B:S.91, B:D.145, B:D.145, B:D.145 Salt bridges: B:D.145 pi-Stacking: B:F.144, B:F.144 pi-Cation interactions: B:F.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riegert, A.S. et al., Biochemical Characterization of WbkC, an N-Formyltransferase from Brucella melitensis. Biochemistry (2017)

Release Date

2017-07-05

Peptides

Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase