SMTL ID : 3wxo.1

Crystal structure of isoniazid bound KatG catalase peroxidase from Synechococcus elongatus PCC7942

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 22 residues within 4Å: Chain A: G.77, L.78, I.80, R.81, W.84, V.213, P.215, F.235, L.248, T.249, G.252, H.253, G.256, K.257, C.258, H.259, T.297, S.298, W.304, A.364, F.392, W.396 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.80, A:R.81, A:W.84, A:W.84, A:W.84, A:V.213, A:F.235, A:L.248, A:F.392, A:W.396 Hydrogen bonds: A:K.257, A:H.259, A:S.298 Water bridges: A:D.71, A:R.81, A:N.117, A:H.259 Salt bridges: A:R.81, A:H.259, A:H.259 pi-Stacking: A:W.84 Metal complexes: A:H.253, H2O.19 HEM.9: 22 residues within 4Å: Chain B: G.77, L.78, I.80, R.81, W.84, V.213, P.215, F.235, L.248, T.249, G.252, H.253, G.256, K.257, C.258, H.259, T.297, S.298, W.304, A.364, F.392, W.396 23 PLIP interactions: 22 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:I.80, B:R.81, B:W.84, B:W.84, B:W.84, B:V.213, B:F.235, B:L.248, B:F.392, B:W.396 Hydrogen bonds: B:K.257, B:H.259, B:T.297, B:S.298 Water bridges: B:R.81, B:N.117, B:H.259 Salt bridges: B:R.81, B:H.259, B:H.259 pi-Stacking: B:W.84 Metal complexes: B:H.253, H2O.38

6 x NIZ: pyridine-4-carbohydrazide(Non-covalent)

NIZ.2: 10 residues within 4Å: Chain A: W.67, W.68, K.120, L.281, W.283, I.284, N.285, G.290, I.291 Chain B: R.652 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.284, A:I.291 Hydrogen bonds: A:K.120, A:W.283, A:N.285, B:R.652, B:R.652 Water bridges: A:G.290 NIZ.3: 6 residues within 4Å: Chain A: P.113, D.114, T.116, V.183, T.297, S.298 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.214, A:N.214, A:E.216 NIZ.4: 3 residues within 4Å: Chain A: N.261, E.301, R.357 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.261, A:R.357 Water bridges: A:R.357, A:R.357, A:R.357, A:N.358 NIZ.10: 10 residues within 4Å: Chain A: R.652 Chain B: W.67, W.68, K.120, L.281, W.283, I.284, N.285, G.290, I.291 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.284, B:I.291 Hydrogen bonds: B:K.120, B:W.283, B:N.285, A:R.652, A:R.652 Water bridges: B:G.290 NIZ.11: 6 residues within 4Å: Chain B: P.113, D.114, T.116, V.183, T.297, S.298 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.114 Water bridges: B:N.214, B:N.214, B:E.216, B:E.216 NIZ.12: 3 residues within 4Å: Chain B: N.261, E.301, R.357 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.261, B:R.357 Water bridges: B:R.357, B:R.357, B:R.357, B:N.358

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

NA.5: 5 residues within 4Å: Chain A: G.95, R.96, G.97, D.403, S.466 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.97 Water bridges: A:G.97, A:G.97 NA.6: 5 residues within 4Å: Chain A: T.254, T.305, H.307, Q.310, D.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.312 Water bridges: A:H.307 NA.7: 2 residues within 4Å: Chain A: R.30, N.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.35 NA.8: 3 residues within 4Å: Chain A: D.685, N.686 Chain B: N.134 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.134, A:D.685 NA.13: 5 residues within 4Å: Chain B: G.95, R.96, G.97, D.403, S.466 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.403, B:S.466 Water bridges: B:G.97, B:G.97 NA.14: 5 residues within 4Å: Chain B: T.254, T.305, H.307, Q.310, D.312 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.305, B:D.312 Water bridges: B:H.307 NA.15: 2 residues within 4Å: Chain B: R.30, N.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.30 NA.16: 3 residues within 4Å: Chain A: N.134 Chain B: D.685, N.686 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.134, B:D.685

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kamachi, S. et al., The crystal structure of isoniazid-bound KatG catalase-peroxidase from Synechococcus elongatus PCC7942. Febs J. (2015)

Release Date

2015-01-21

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Catalase-peroxidase