SMTL ID : 8dwr.2 (1 other biounit)

Crystal structure of the L333V variant of catalase-peroxidase from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: P.106, L.107, I.109, R.110, X.113, V.236, P.238, I.254, F.258, L.271, I.272, G.275, H.276, F.278, G.279, K.280, T.281, H.282, T.320, S.321, W.327, T.386, F.414, W.418 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:I.109, A:R.110, A:P.238, A:I.254, A:F.258, A:L.271, A:I.272, A:I.272, A:T.281, A:W.327, A:F.414, A:W.418 Hydrogen bonds: A:K.280, A:H.282, A:S.321 Water bridges: A:D.100, A:D.100, A:R.110, A:H.282 Salt bridges: A:R.110, A:H.282, A:H.282 Metal complexes: A:H.276 HEM.6: 23 residues within 4Å: Chain B: P.106, L.107, I.109, R.110, X.113, V.236, P.238, F.258, L.271, I.272, G.275, H.276, F.278, G.279, K.280, T.281, H.282, T.320, S.321, W.327, T.386, F.414, W.418 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:I.109, B:R.110, B:P.238, B:F.258, B:L.271, B:I.272, B:T.281, B:W.327, B:F.414, B:W.418 Hydrogen bonds: B:K.280, B:H.282, B:S.321 Water bridges: B:R.110, B:S.146, B:H.282 Salt bridges: B:R.110, B:H.282, B:H.282 Metal complexes: B:H.276

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 7 residues within 4Å: Chain A: A.262, K.420, R.424, W.444, D.586, E.588, S.589 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.586, A:S.589 Water bridges: A:K.420, A:R.424, A:R.424, A:E.588, A:E.588 Salt bridges: A:K.420, A:R.424, A:D.586, A:D.586 EPE.4: 10 residues within 4Å: Chain A: W.45, P.46, N.47, R.48, E.613, Y.614, R.699 Chain B: A.296, A.297, L.299 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:A.297 Hydrogen bonds: A:N.47, A:N.47, A:E.613, A:R.699

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: G.124, R.125, G.126, S.492, D.493 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.492 NA.7: 4 residues within 4Å: Chain B: G.124, R.125, G.126, S.492 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.492 Water bridges: B:G.126, B:G.126, B:D.425

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 4 residues within 4Å: Chain A: D.85, E.88, V.89, Q.94 No protein-ligand interaction detected (PLIP) PGE.8: 4 residues within 4Å: Chain B: E.88, V.89, Q.94, P.156 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uribe-Vazquez, B. et al., Characterization of a catalase-peroxidase variant (L333V-KatG) identified in an INH-resistant Mycobacterium tuberculosis clinical isolate. Biochem Biophys Rep (2024)

Release Date

2023-08-02

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Catalase-peroxidase

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