SMTL ID : 5sx1.1

Crystal structure of D141E variant of B. pseudomallei KatG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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, 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: OXY.3, OXY.4 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:I.87, A:W.91, A:W.91, A:W.91, A:P.221, A:F.241, A:L.254, 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 HEM.8: 27 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, W.310, L.366, T.368, F.396, W.400 Ligands: OXY.10, OXY.11, OXY.14 27 PLIP interactions: 27 interactions with chain B, Hydrophobic interactions: B:I.87, B:R.88, B:W.91, B:W.91, B:W.91, 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: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: 5 residues within 4Å: Chain A: G.102, R.103, G.104, D.407, 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: 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:S.474

5 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 5 residues within 4Å: Chain A: R.88, H.92, E.121 Ligands: HEM.1, OXY.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.88 OXY.4: 6 residues within 4Å: Chain A: R.88, W.91, H.92, E.121 Ligands: HEM.1, OXY.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.91, A:E.121 OXY.10: 5 residues within 4Å: Chain B: R.88, H.92, E.121 Ligands: HEM.8, OXY.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.88, B:E.121 OXY.11: 5 residues within 4Å: Chain B: W.91, H.92, E.121 Ligands: HEM.8, OXY.10 No protein-ligand interaction detected (PLIP) OXY.14: 5 residues within 4Å: Chain B: E.121, I.217, Y.218, V.219 Ligands: HEM.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.217, B:Y.218, B:V.219, B:V.219

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

MPD.5: 5 residues within 4Å: Chain A: P.120, A.123, L.189, W.289, T.303 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.189 Hydrogen bonds: A:W.289 MPD.6: 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.12: 7 residues within 4Å: Chain B: 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 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 PO4.13: 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