SMTL ID : 5v00.1

Structure of HutD from Pseudomonas fluorescens SBW25 (Formate condition)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: W.24, N.26, G.59, F.60, S.61 Ligands: FMT.2, FMT.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.59, A:S.61 Water bridges: A:K.25, A:N.26, A:S.61, A:S.61 GOL.12: 6 residues within 4Å: Chain B: W.24, N.26, G.59, F.60, S.61 Ligands: FMT.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.61

10 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 5 residues within 4Å: Chain A: A.52, F.60, R.68, N.117 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.68, A:R.68, A:N.117 FMT.3: 4 residues within 4Å: Chain A: F.63, R.68, N.117, I.119 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.68, A:R.68, A:N.117 Water bridges: A:R.48, A:S.50 FMT.4: 3 residues within 4Å: Chain A: P.23 Chain B: R.36, R.48 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.36, B:R.36, B:R.48 FMT.5: 5 residues within 4Å: Chain A: W.24, K.25 Chain B: V.20, M.22 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.25 Water bridges: A:P.23, A:N.26, A:S.61 FMT.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.7: 4 residues within 4Å: Chain B: F.60, R.68, N.117 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.68, B:R.68, B:N.117 FMT.8: 5 residues within 4Å: Chain A: T.40, G.41 Chain B: R.15, K.160, G.162 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.41, B:R.15, B:G.162 Water bridges: A:T.40, A:L.42 FMT.9: 7 residues within 4Å: Chain B: T.81, V.82, D.83, G.84, Q.103, V.104, S.105 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.84, B:Q.103 FMT.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.11: 4 residues within 4Å: Chain B: F.63, R.68, N.117, I.119 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.68, B:N.117 Water bridges: B:S.50, B:R.68, B:L.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gerth, M.L. et al., Crystal structure of a bicupin protein HutD involved in histidine utilization in Pseudomonas. Proteins (2017)

Release Date

2017-03-15

Peptides

Uncharacterized protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uncharacterized protein

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