SMTL ID : 6b9b.1

Crystal structure of the catalase-peroxidase from B. pseudomallei with maltose bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 6 residues within 4Å: Chain A: R.486, A.502, L.505, E.506, E.509, L.527 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.502, A:E.506, A:E.509 Water bridges: A:R.486 GLC-GLC.2: 4 residues within 4Å: Chain B: R.486, L.487, E.509, Q.563 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.486 Water bridges: B:R.486, B:R.486, B:Q.563

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

HEM.3: 26 residues within 4Å: Chain A: 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, L.306, W.310, L.366, T.368, F.396, W.400 Ligands: OXY.6 26 PLIP interactions: 26 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: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 Metal complexes: A:H.259 HEM.10: 26 residues within 4Å: Chain B: 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, W.310, L.366, T.368, F.396, W.400 Ligands: OXY.13 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:I.87, B:P.221, B:I.237, 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.4: 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.11: 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:G.102

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

CL.5: 3 residues within 4Å: Chain A: G.104, E.178, V.180 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: G.104, E.178, V.180 Ligand excluded by PLIP

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.6: 5 residues within 4Å: Chain A: R.88, X.91, H.92, D.121 Ligands: HEM.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.88, A:D.121 OXY.13: 5 residues within 4Å: Chain B: R.88, X.91, H.92, D.121 Ligands: HEM.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.88, B:D.121 Water bridges: B:D.121

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 PO4.14: 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

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

MPD.8: 4 residues within 4Å: Chain A: P.120, A.270, T.303, S.304 No protein-ligand interaction detected (PLIP) MPD.9: 4 residues within 4Å: Chain A: D.63, P.134, I.135, K.138 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.63, A:K.138 Hydrogen bonds: A:P.134 MPD.15: 5 residues within 4Å: Chain B: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loewen, P.C. et al., KatG-Mediated Oxidation Leading to Reduced Susceptibility of Bacteria to Kanamycin. ACS Omega (2018)

Release Date

2018-07-04

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase

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