SMTL ID : 5wol.1

Crystal structure of dihydrodipicolinate reductase DapB from Coxiella burnetii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 22 residues within 4Å: Chain A: N.8, G.9, N.11, G.12, K.13, M.14, G.35, R.36, F.55, T.56, T.57, S.60, N.64, G.78, T.79, T.80, A.104, P.105, N.106, F.107, T.214 Ligands: 6PC.4 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:N.8, A:N.11, A:N.11, A:K.13, A:M.14, A:S.60, A:S.60, A:N.64, A:G.78, A:T.80, A:F.107 Water bridges: A:G.12, A:G.12, A:G.12, A:G.15, A:R.36, A:R.36, A:R.36, A:T.57, A:T.80, A:S.108, A:R.211 Salt bridges: A:K.13, A:K.13, A:R.36 pi-Stacking: A:F.55

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: K.138, S.143, G.144, T.145 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.144, A:T.145, A:T.145, A:T.145 Water bridges: A:K.138 Salt bridges: A:K.138 SO4.3: 4 residues within 4Å: Chain A: Q.137, K.138, I.139, D.140 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.139, A:D.140 Water bridges: A:K.138, A:K.138 Salt bridges: A:K.138

2 x 6PC: PYRIDINE-2-CARBOXYLIC ACID(Non-covalent)

6PC.4: 6 residues within 4Å: Chain A: H.135, F.188, R.211, C.213, T.214 Ligands: NAP.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.188, A:F.188, A:R.211, A:T.214 Water bridges: A:R.211 Salt bridges: A:H.135, A:R.211 6PC.5: 6 residues within 4Å: Chain A: P.105, N.106, G.144, T.145, K.148, Y.233 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.105, A:N.106, A:K.148 Water bridges: A:K.148, A:K.148, A:E.236 Salt bridges: A:K.148

1 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)

PE3.6: 1 residues within 4Å: Chain A: D.207 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stogios, P.J., Crystal structure of dihydrodipicolinate reductase DapB from Coxiella burnetii. To Be Published

Release Date

2017-08-16

Peptides

4-hydroxy-tetrahydrodipicolinate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

4-hydroxy-tetrahydrodipicolinate reductase