SMTL ID : 5vyr.1

Crystal structure of the WbkC formyl transferase from Brucella melitensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x B62: (6R)-2-amino-6-methyl-5,6,7,8-tetrahydropteridin-4(3H)-one(Non-covalent)

B62.1: 14 residues within 4Å: Chain A: S.86, Y.89, S.91, L.92, I.93, L.98, N.107, H.138, M.140, D.141, E.142, N.143, F.144, D.145 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.93, A:I.93, A:I.93, A:N.107, A:D.145 Water bridges: A:D.141, A:T.146 B62.5: 14 residues within 4Å: Chain B: S.86, Y.89, S.91, L.92, I.93, L.98, N.107, H.138, M.140, D.141, E.142, N.143, F.144, D.145 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:I.93, B:I.93, B:I.93, B:N.107, B:D.145 Water bridges: B:D.141, B:T.146

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

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: S.111, L.112, Y.116, T.133 Ligand excluded by PLIP

3 x GMP: GUANOSINE(Non-covalent)

GMP.4: 4 residues within 4Å: Chain A: M.227, F.229, F.232, P.233 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.227, A:M.227 Water bridges: A:F.229 pi-Stacking: A:F.232, A:F.232 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:R.90, B:H.109, B:G.118, B:R.203 Water bridges: B:L.92, B:G.118, 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 GMP.7: 5 residues within 4Å: Chain B: L.205, M.227, F.229, F.232, P.233 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.227 pi-Stacking: B:F.232

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