SMTL ID : 6omz.1

Crystal Structure of Dihydropteroate synthase from Mycobacterium smegmatis with bound 6-hydroxymethylpterin-monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 8 residues within 4Å: Chain A: T.69, R.70, H.157, G.197, F.198, K.229, R.230 Ligands: PMM.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.198, A:K.229 Hydrogen bonds: A:T.69, A:R.230 Water bridges: A:T.69, A:T.69, A:R.70, A:F.231 Salt bridges: A:R.70, A:R.70, A:H.157 CIT.4: 6 residues within 4Å: Chain A: T.201, A.202, E.203, R.230, F.231, T.234 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.234 Hydrogen bonds: A:A.202, A:R.230, A:R.230, A:T.234 Salt bridges: A:R.230, A:R.230

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 4 residues within 4Å: Chain A: M.104, A.128, W.148, S.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.150 pi-Cation interactions: A:W.148

1 x PMM: PTERIN-6-YL-METHYL-MONOPHOSPHATE(Non-covalent)

PMM.3: 13 residues within 4Å: Chain A: R.70, D.102, N.121, V.123, M.146, D.193, F.198, L.223, G.225, K.229, R.269, H.271 Ligands: CIT.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.121, A:N.121, A:K.229 Water bridges: A:R.70, A:R.70, A:R.70, A:R.70, A:G.195, A:G.225, A:S.227, A:R.269, A:R.269, A:R.269, A:R.269 Salt bridges: A:R.70, A:D.193, A:R.269, A:H.271 pi-Cation interactions: A:R.269

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

EDO.5: 4 residues within 4Å: Chain A: A.56, A.57, V.277, K.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.281 EDO.6: 7 residues within 4Å: Chain A: G.125, G.126, A.133, W.143, A.176, A.179, A.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.125 EDO.7: 5 residues within 4Å: Chain A: P.78, G.79, A.82, D.107, V.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.78 EDO.8: 3 residues within 4Å: Chain A: D.164, V.166, A.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.164 EDO.9: 3 residues within 4Å: Chain A: P.142, P.221, W.266 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain A: S.124, G.125, R.127, M.146, H.147, W.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.124, A:W.148 Water bridges: A:R.127, A:E.172 EDO.11: 5 residues within 4Å: Chain A: V.55, A.59, Q.60, I.97, T.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.98, A:T.98 Water bridges: A:T.98 EDO.12: 3 residues within 4Å: Chain A: R.149, P.160, G.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.149, A:G.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bolejack, M.J. et al., Crystal Structure of Dihydropteroate synthase from Mycobacterium smegmatis with bound 6-hydroxymethylpterin-monophosphate. to be published

Release Date

2019-05-08

Peptides

Dihydropteroate synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydropteroate synthase