SMTL ID : 5sx7.1

Crystal structure of catalase-peroxidase KatG of B. pseudomallei at pH 8.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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, 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.3 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:I.87, A:R.88, 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: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: 25 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 22 PLIP interactions: 22 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:G.84, 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: 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:G.104 NA.10: 4 residues within 4Å: Chain B: G.102, R.103, G.104, S.474 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.474 Water bridges: B:G.104, B:E.108

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 5 residues within 4Å: Chain A: R.88, X.91, H.92, D.121 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.88 OXY.11: 5 residues within 4Å: Chain B: R.88, X.91, H.92, D.121 Ligands: HEM.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.88, B:H.92

4 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 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.189 MPD.5: 3 residues within 4Å: Chain A: D.63, P.134, K.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.134 Water bridges: A:K.138 MPD.12: 5 residues within 4Å: Chain B: P.120, A.123, A.270, T.303, S.304 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.120, B:A.270 Hydrogen bonds: B:W.289 MPD.13: 4 residues within 4Å: Chain B: G.547, H.548, A.549, E.706 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.548, B:E.706 Hydrogen bonds: B:G.547, B:E.706, B:R.710

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

TRS.6: 9 residues within 4Å: Chain A: A.100, D.101, R.472, V.573, L.574, E.575, P.576, K.600, L.603 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.100, A:R.472, A:R.472, A:K.600 Water bridges: A:S.469, A:L.574, A:E.575 TRS.7: 8 residues within 4Å: Chain A: D.40, P.41, M.42, G.43 Chain B: P.609, Y.699, K.707, D.711 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.41, B:K.707, B:K.707 TRS.8: 8 residues within 4Å: Chain A: P.609, Y.699, K.707, D.711 Chain B: D.40, P.41, M.42, G.43 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:M.42, A:K.707, A:K.707 Water bridges: B:G.43, A:S.607, A:Y.699 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carpena, X. et al., Roles for Arg426 and Trp111 in the modulation of NADH oxidase activity of the catalase-peroxidase KatG from Burkholderia pseudomallei inferred from pH-induced structural changes. Biochemistry (2006)

Release Date

2016-08-31

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase

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