SMTL ID : 5l05.1

Crystal structure of catalase-peroxidase KATG of burkholderia pseudomallei treated with INH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x HP5: Peroxidized Heme Form 2(Non-covalent)

HP5.1: 26 residues within 4Å: Chain A: G.84, L.85, I.87, R.88, W.91, Y.218, 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, T.368, F.396, W.400 Ligands: OXY.3 27 PLIP interactions: 26 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:L.254, A:I.255, A:T.264, A:L.306, A:W.310, A:F.396, A:W.400 Hydrogen bonds: A:Y.218, A:V.219, 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 Metal complexes: A:H.259, H2O.14 HP5.6: 26 residues within 4Å: Chain B: G.84, L.85, I.87, R.88, W.91, Y.218, 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, T.368, F.396, W.400 Ligands: OXY.8 31 PLIP interactions: 30 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:I.87, B:R.88, B:W.91, B:W.91, B:W.91, B:V.219, B:P.221, B:P.221, B:L.254, B:I.255, B:T.264, B:L.306, B:W.310, B:F.396, B:W.400 Hydrogen bonds: B:Y.218, B:V.219, B:K.263, B:H.265, B:T.303, B:S.304 Water bridges: B:G.84, B:R.88, B:R.88, B:V.219, B:H.265 Salt bridges: B:R.88, B:H.265, B:H.265 Metal complexes: B:H.259, H2O.54

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

NA.2: 5 residues within 4Å: Chain A: G.102, R.103, G.104, D.407, S.474 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.407, A:D.407 NA.7: 4 residues within 4Å: Chain B: G.102, R.103, G.104, S.474 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.407 Water bridges: B:E.108

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 4 residues within 4Å: Chain A: R.88, H.92, D.121 Ligands: HP5.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.88, A:R.88, A:D.121 OXY.8: 4 residues within 4Å: Chain B: R.88, H.92, D.121 Ligands: HP5.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.88, B:R.88, B:D.121 Water bridges: B:D.121

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

MPD.4: 5 residues within 4Å: Chain A: P.120, A.123, L.189, T.303, S.304 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.120, A:A.123, A:L.189 Hydrogen bonds: A:T.303 MPD.5: 4 residues within 4Å: Chain A: D.63, P.134, I.135, K.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.134 Water bridges: A:K.138 MPD.9: 5 residues within 4Å: Chain B: L.189, A.270, W.289, T.303, S.304 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.270 Hydrogen bonds: B:W.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carpena, X. et al., Catalase-peroxidase KatG of Burkholderia pseudomallei at 1.7A resolution. J. Mol. Biol. (2003)

Release Date

2016-08-24

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase

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