SMTL ID : 5sxs.1

Crystal structure of catalase-peroxidase KatG with isonicotinic acid hydrazide and AMP bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 28 residues within 4Å: Chain A: G.84, L.85, I.87, R.88, W.91, V.219, P.221, I.237, F.241, L.254, I.255, G.258, H.259, F.261, G.262, K.263, T.264, H.265, T.303, S.304, L.306, W.310, L.366, T.368, F.396, W.400 Ligands: OXY.4, OXY.5 32 PLIP interactions: 31 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.87, A:R.88, A:W.91, A:W.91, A:W.91, A:P.221, A:P.221, A:I.237, A:F.241, A:L.254, A:I.255, A:I.255, A:T.264, A:L.306, A:W.310, A:L.366, A:F.396, A:W.400 Hydrogen bonds: A:K.263, A:H.265, A:S.304 Water bridges: A:D.78, A:D.78, A:G.84, A:R.88, A:H.265 Salt bridges: A:R.88, A:H.265, A:H.265 pi-Stacking: A:W.91 Metal complexes: A:H.259, H2O.9 HEM.8: 26 residues within 4Å: Chain B: G.84, L.85, I.87, R.88, W.91, V.219, P.221, L.254, I.255, G.258, H.259, F.261, G.262, K.263, T.264, H.265, T.303, S.304, L.306, W.310, L.366, T.368, F.396, W.400 Ligands: OXY.11, OXY.12 28 PLIP interactions: 27 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:I.87, B:R.88, B:W.91, B:W.91, B:P.221, B:L.254, B:I.255, B:I.255, B:T.264, B:L.306, B:W.310, B:L.366, B:F.396, B:W.400 Hydrogen bonds: B:K.263, B:H.265, B:T.303, B:S.304 Water bridges: B:G.84, B:R.88, B:R.88, B:H.265 Salt bridges: B:R.88, B:H.265, B:H.265 pi-Stacking: B:W.91 Metal complexes: B:H.259, H2O.33

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

NA.2: 4 residues within 4Å: Chain A: G.102, R.103, G.104, S.474 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.407, A:D.407 Water bridges: A:E.108 NA.9: 5 residues within 4Å: Chain B: G.102, R.103, G.104, S.474, D.475 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.407 Water bridges: B:E.108

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

CL.3: 3 residues within 4Å: Chain A: G.104, E.178, V.180 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: G.104, E.178, V.180 Ligands: NIZ.13 Ligand excluded by PLIP

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 5 residues within 4Å: Chain A: R.88, H.92, D.121 Ligands: HEM.1, OXY.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.88 OXY.5: 4 residues within 4Å: Chain A: W.91, H.92 Ligands: HEM.1, OXY.4 6 PLIP interactions: 6 interactions with chain A Water bridges: A:W.91, A:H.92, A:I.217, A:Y.218, A:Y.218, A:Y.218 OXY.11: 5 residues within 4Å: Chain B: R.88, H.92, D.121 Ligands: HEM.8, OXY.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.88, B:H.92 Water bridges: B:D.121, B:D.121 OXY.12: 5 residues within 4Å: Chain B: W.91, H.92, D.121 Ligands: HEM.8, OXY.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.92 Water bridges: B:I.217, B:I.217, B:Y.218, B:Y.218

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 3 residues within 4Å: Chain A: K.360, H.361, R.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.362 Salt bridges: A:H.361, A:R.362 PO4.15: 3 residues within 4Å: Chain B: K.360, H.361, R.362 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.360, B:R.362 Salt bridges: B:H.361, B:R.362

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.7: 4 residues within 4Å: Chain A: A.270, V.273, T.303, S.304 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.270, A:V.273 Hydrogen bonds: A:W.289

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

NIZ.13: 11 residues within 4Å: Chain B: R.103, E.108, E.178, D.179, V.180, G.473, S.474, Q.602, L.603, T.605 Ligands: CL.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.103, B:E.178, B:E.178, B:Q.602 Water bridges: B:G.104

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.14: 7 residues within 4Å: Chain B: P.120, A.123, A.270, V.273, T.303, S.304, G.305 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.123, B:A.270 Water bridges: B:W.289

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.16: 5 residues within 4Å: Chain B: D.202, R.203, D.229, A.232, R.235 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.202, B:D.202 Water bridges: B:R.235, B:R.235 Salt bridges: B:R.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wiseman, B. et al., Isonicotinic acid hydrazide conversion to Isonicotinyl-NAD by catalase-peroxidases. J. Biol. Chem. (2010)

Release Date

2016-09-07

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase

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