SMTL ID : 5ksk.1

Crystal structure of the catalase-peroxidase from B. pseudomallei treated with acetate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 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.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: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.8: 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 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:I.87, B:R.88, 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.407, A:D.407 NA.9: 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 CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: G.104, E.178, V.180 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: G.104, E.178, V.180 Ligand excluded by PLIP

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 5 residues within 4Å: Chain A: R.88, X.91, H.92, D.121 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.88, A:D.121 OXY.11: 5 residues within 4Å: Chain B: R.88, X.91, H.92, D.121 Ligands: HEM.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.88, B:D.121 Water bridges: B:D.121

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

MPD.5: 3 residues within 4Å: Chain A: D.63, P.134, K.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.134 MPD.6: 6 residues within 4Å: Chain A: P.120, A.123, L.189, W.289, T.303, S.304 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.120, A:A.123, A:L.189 MPD.7: 3 residues within 4Å: Chain A: D.643, V.646, N.647 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.646 Water bridges: A:R.636, A:N.647, A:N.647 MPD.12: 3 residues within 4Å: Chain B: R.486, L.487, E.509 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.509 MPD.13: 5 residues within 4Å: Chain B: P.120, A.270, W.289, T.303, S.304 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Machuqueiro, M. et al., The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine. Biochemistry (2017)

Release Date

2017-04-26

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase

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