SMTL ID : 6v33.1

X-ray structure of a sugar N-formyltransferase from Pseudomonas congelans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x 0FX: dTDP-4-amino-4,6-dideoxyglucose(Non-covalent)

0FX.1: 12 residues within 4Å: Chain A: N.21, H.87, K.89, P.107, W.116, Y.117, Q.119, Y.163, Y.203, H.229, F.232, N.234 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.107, A:Y.117, A:F.232 Hydrogen bonds: A:N.21, A:K.89, A:Q.119, A:Y.203, A:N.234, A:N.234 Water bridges: A:D.20, A:Q.119, A:S.159 Salt bridges: A:H.87, A:H.87, A:K.89, A:K.89 pi-Stacking: A:Y.117, A:F.232 0FX.4: 12 residues within 4Å: Chain B: N.21, H.87, C.88, K.89, W.116, Y.117, Q.119, Y.163, Y.203, H.229, F.232, N.234 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.117, B:F.232 Hydrogen bonds: B:N.21, B:K.89, B:Q.119, B:Y.203, B:N.234, B:N.234 Water bridges: B:D.20, B:K.89, B:S.159 Salt bridges: B:H.87, B:H.87, B:K.89 pi-Stacking: B:Y.117, B:F.232

2 x FOL: FOLIC ACID(Non-covalent)

FOL.2: 14 residues within 4Å: Chain A: S.85, C.88, K.89, Q.90, L.91, F.92, N.104, H.134, M.136, D.137, E.138, A.139, I.140, D.141 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.140, A:I.140 Hydrogen bonds: A:C.88, A:F.92, A:F.92, A:F.92, A:D.141, A:D.141 Water bridges: A:K.68, A:N.104, A:H.134, A:D.137 FOL.5: 16 residues within 4Å: Chain B: S.85, C.88, K.89, Q.90, L.91, F.92, V.97, N.104, W.116, H.134, M.136, D.137, E.138, A.139, I.140, D.141 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.140 Hydrogen bonds: B:C.88, B:F.92, B:F.92, B:D.141 Water bridges: B:L.91

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

EDO.3: 7 residues within 4Å: Chain A: S.155, R.218, I.221, N.222, R.225 Chain B: L.211, F.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.218 EDO.6: 7 residues within 4Å: Chain A: L.211, F.237 Chain B: S.155, R.218, I.221, N.222, R.225 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Girardi, N.M. et al., Misannotations of the genes encoding sugar N-formyltransferases. Protein Sci. (2020)

Release Date

2020-01-08

Peptides

dTDP-4-amino-4,6-dideoxyglucose formyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

dTDP-4-amino-4,6-dideoxyglucose formyltransferase