SMTL ID : 5syj.1

Crystal structure of the D141A variant of B. pseudomallei KatGin complex with isoniazid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: G.84, L.85, I.87, R.88, W.91, V.219, P.221, 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: NIZ.10 28 PLIP interactions: 28 interactions with chain A, Hydrophobic interactions: A:I.87, A:R.88, A:W.91, A:W.91, 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: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 HEM.11: 26 residues within 4Å: Chain B: G.84, L.85, I.87, R.88, W.91, V.219, P.221, 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: NIZ.20 28 PLIP interactions: 28 interactions with chain B, Hydrophobic interactions: B:I.87, B:R.88, B:W.91, B:W.91, B:P.221, B:P.221, B:F.241, 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:H.265 Salt bridges: B:R.88, B:H.265, B:H.265 pi-Stacking: B:W.91 Metal complexes: B:H.259

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

NA.2: 4 residues within 4Å: Chain A: G.102, R.103, G.104, S.474 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.407, A:D.407 NA.12: 4 residues within 4Å: Chain B: G.102, R.103, G.104, S.474 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.407

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

CL.3: 4 residues within 4Å: Chain A: G.104, E.178, V.180 Ligands: NIZ.9 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: G.104, E.178, V.180 Ligands: NIZ.19 Ligand excluded by PLIP

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

MPD.4: 4 residues within 4Å: Chain A: D.63, P.134, I.135, K.138 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.138 Hydrogen bonds: A:P.134 MPD.5: 5 residues within 4Å: Chain A: A.123, L.189, A.270, V.273, T.303 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.123, A:A.270, A:V.273 Hydrogen bonds: A:T.303 MPD.6: 6 residues within 4Å: Chain A: P.609, E.610, Y.699, D.711 Chain B: P.41, M.42 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.609 Hydrogen bonds: B:P.41 Water bridges: B:K.44 MPD.8: 2 residues within 4Å: Chain A: D.643, N.647 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.647, A:N.647 Water bridges: A:R.636 MPD.14: 4 residues within 4Å: Chain B: A.123, A.270, T.303, S.304 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.123, B:A.270 Water bridges: B:V.273 MPD.15: 6 residues within 4Å: Chain B: G.547, H.548, A.549, E.706, R.710 Ligands: MPD.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.549 MPD.16: 5 residues within 4Å: Chain B: N.721, L.722, R.724, F.725, A.728 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.728 Hydrogen bonds: B:R.724, B:R.724 MPD.17: 5 residues within 4Å: Chain B: K.544, G.547, H.548, A.549 Ligands: MPD.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.544, B:A.549

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

PO4.7: 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 PO4.18: 2 residues within 4Å: Chain B: H.361, R.362 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.362 Salt bridges: B:H.361, B:R.362

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

NIZ.9: 11 residues within 4Å: Chain A: R.103, E.108, E.178, D.179, V.180, G.473, S.474, Q.602, L.603, T.605 Ligands: CL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.103, A:R.103, A:E.178, A:Q.602 Water bridges: A:G.104 NIZ.10: 8 residues within 4Å: Chain A: R.88, W.91, H.92, A.121, L.216, P.221, S.304 Ligands: HEM.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.88, A:W.91 Water bridges: A:W.91, A:H.92 NIZ.19: 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.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.103, B:R.103, B:E.178, B:Q.602 Water bridges: B:G.104 NIZ.20: 8 residues within 4Å: Chain B: R.88, W.91, H.92, A.121, L.216, P.221, S.304 Ligands: HEM.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.88, B:W.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vidossich, P. et al., Binding of the antitubercular pro-drug isoniazid in the heme access channel of catalase-peroxidase (KatG). A combined structural and metadynamics investigation. J Phys Chem B (2014)

Release Date

2016-09-21

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase

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