SMTL ID : 5sx2.1

Crystal structure of the D141E mutant of B. pseudomallei KatG at pH 8.0.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 27 residues within 4Å: Chain A: G.84, L.85, I.87, R.88, X.91, E.121, 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, OXY.4 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:I.87, A:R.88, A:P.221, A:P.221, A:F.241, A:L.254, A:I.255, A:I.255, A:T.264, A:L.306, A:W.310, 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 Metal complexes: A:H.259 HEM.9: 26 residues within 4Å: Chain B: G.84, L.85, I.87, R.88, X.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, W.310, L.366, T.368, F.396, W.400 Ligands: OXY.11, OXY.12 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:I.87, B:P.221, B:F.241, B:L.254, B:I.255, B:I.255, B:T.264, 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:R.88, B:H.265 Salt bridges: B:R.88, B:H.265, B:H.265 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.407, A:D.407 Water bridges: A:G.104 NA.10: 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:S.474 Water bridges: B:E.108

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 5 residues within 4Å: Chain A: E.121, I.217, Y.218, V.219 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.217, A:Y.218, A:V.219 OXY.4: 5 residues within 4Å: Chain A: R.88, X.91, H.92, E.121 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.121 Water bridges: A:R.88 OXY.11: 7 residues within 4Å: Chain B: X.91, E.121, L.216, I.217, Y.218, V.219 Ligands: HEM.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.121, B:I.217, B:Y.218, B:V.219 OXY.12: 5 residues within 4Å: Chain B: R.88, X.91, H.92, E.121 Ligands: HEM.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.88, B:H.92, B:E.121

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

MPD.5: 5 residues within 4Å: Chain A: A.123, L.189, W.289, T.303, S.304 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.189 Hydrogen bonds: A:W.289, A:T.303 MPD.6: 3 residues within 4Å: Chain A: D.63, P.134, K.138 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.138 Hydrogen bonds: A:P.134 MPD.13: 8 residues within 4Å: Chain B: P.120, A.123, L.189, A.270, V.273, W.289, T.303, S.304 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.270, B:V.273 Hydrogen bonds: B:W.289

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 9 residues within 4Å: Chain A: A.100, D.101, R.472, V.573, L.574, E.575, P.576, K.600, L.603 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.472, A:R.472, A:V.573, A:K.600 Water bridges: A:S.469, A:L.574 TRS.14: 9 residues within 4Å: Chain B: A.100, D.101, R.472, V.573, L.574, E.575, P.576, K.600, L.603 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.100, B:R.472, B:R.472, B:K.600, B:K.600

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

PO4.8: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deemagarn, T. et al., Two alternative substrate paths for compound I formation and reduction in catalase-peroxidase KatG from Burkholderia pseudomallei. Proteins (2007)

Release Date

2016-09-07

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase