SMTL ID : 5vyq.1

Crystal structure of the N-formyltransferase Rv3404c from mycobacterium tuberculosis in complex with YDP-Qui4N and folinic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

FON.1: 17 residues within 4Å: Chain A: S.81, C.84, K.85, Q.86, R.87, F.88, N.100, W.112, I.132, D.133, Q.135, L.136, D.137, L.195, K.196 Ligands: 0FX.2, LI.11 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.112, A:L.136, A:L.136, A:K.196 Hydrogen bonds: A:Q.86, A:F.88, A:F.88, A:F.88, A:N.100, A:D.137, A:D.137, A:K.196 Water bridges: A:R.87, A:D.133, A:H.138 Salt bridges: A:K.196

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

0FX.2: 18 residues within 4Å: Chain A: N.30, H.83, C.84, K.85, H.102, G.111, W.112, F.113, P.114, Q.115, D.137, S.155, Y.159, H.225, F.228, N.230 Ligands: FON.1, LI.11 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.113, A:F.113, A:F.228 Hydrogen bonds: A:N.30, A:H.102, A:F.113, A:Q.115, A:N.230, A:N.230 Water bridges: A:K.85, A:K.85, A:N.100, A:S.155 Salt bridges: A:H.83, A:H.83, A:K.85, A:K.85, A:K.85 pi-Stacking: A:F.228

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

EDO.3: 6 residues within 4Å: Chain A: S.151, G.214, N.218, R.221 Chain B: L.207, F.233 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.151, A:N.218 Water bridges: A:R.221 EDO.4: 5 residues within 4Å: Chain A: S.154, V.245, V.246, L.247 Ligands: CL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.247 EDO.13: 6 residues within 4Å: Chain A: L.207, F.233 Chain B: S.151, G.214, N.218, R.221 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.151, B:N.218 Water bridges: B:R.221, B:R.221, B:R.221 EDO.14: 7 residues within 4Å: Chain B: C.84, Q.86, N.100, H.130, Q.135, L.136, D.137 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.137 Water bridges: B:C.84, B:H.130, B:D.133, B:D.137

4 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: V.73, Y.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.73 NA.6: 3 residues within 4Å: Chain A: M.21, T.23, D.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.23, A:T.23, A:D.77 NA.10: 1 residues within 4Å: Chain A: Y.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.50, A:Y.50 NA.17: 2 residues within 4Å: Chain B: V.73, Y.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.73

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

CL.7: 6 residues within 4Å: Chain A: S.154, G.156, T.224, H.225, D.226 Ligands: EDO.4 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: R.210 Chain B: R.210, G.211 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: S.154, G.156, T.224, H.225, D.226 Ligand excluded by PLIP

2 x EP1: 3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID(Non-covalent)

EP1.8: 5 residues within 4Å: Chain A: H.225, D.226, D.227, F.228, R.229 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.225, A:D.226, A:R.229 Salt bridges: A:D.227, A:D.227, A:R.229 EP1.16: 5 residues within 4Å: Chain B: H.225, D.226, D.227, F.228, R.229 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.228 Hydrogen bonds: B:H.225, B:R.229 Salt bridges: B:D.227, B:D.227, B:R.229

1 x LI: LITHIUM ION(Non-covalent)

LI.11: 5 residues within 4Å: Chain A: N.100, H.102, D.137 Ligands: FON.1, 0FX.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.102, A:D.137, A:D.137, H2O.1

1 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.12: 10 residues within 4Å: Chain B: N.30, H.83, K.85, F.113, Q.115, Y.159, F.199, H.225, F.228, N.230 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.113, B:F.113 Hydrogen bonds: B:N.30, B:Q.115, B:Y.159, B:Y.159, B:N.230, B:N.230 Water bridges: B:D.29, B:K.85, B:K.85, B:K.85, B:Q.115, B:S.155 Salt bridges: B:H.83, B:K.85, B:K.85 pi-Stacking: B:F.228

1 x K: POTASSIUM ION(Non-covalent)

K.18: 1 residues within 4Å: Chain B: D.94 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.94, H2O.16, H2O.18, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dunsirn, M.M. et al., Biochemical Investigation of Rv3404c from Mycobacterium tuberculosis. Biochemistry (2017)

Release Date

2017-07-12

Peptides

Uncharacterized protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uncharacterized protein