SMTL ID : 8w1y.1 (1 other biounit)

2.30 angstrom resolution intermediate crystal structure of KatG from Mycobacterium tuberculosis with an MYW-OOH cofactor soaked with peroxide for 1 minute

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: P.101, L.102, R.105, X.108, V.231, P.233, I.249, F.253, L.266, I.267, G.270, H.271, F.273, G.274, K.275, T.276, H.277, T.315, S.316, W.322, L.379, T.381, F.409, W.413 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:R.105, A:V.231, A:P.233, A:I.249, A:F.253, A:L.266, A:I.267, A:I.267, A:T.276, A:W.322, A:L.379, A:T.381, A:F.409, A:W.413 Hydrogen bonds: A:K.275, A:H.277, A:S.316 Water bridges: A:D.95, A:D.95, A:D.95, A:R.105, A:S.141 Salt bridges: A:R.105, A:H.277, A:H.277 Metal complexes: A:H.271 HEM.4: 20 residues within 4Å: Chain B: P.101, L.102, R.105, X.108, V.231, P.233, F.253, L.266, G.270, H.271, G.274, K.275, T.276, H.277, T.315, S.316, W.322, L.379, T.381, W.413 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:R.105, B:F.253, B:L.266, B:T.276, B:W.322, B:L.379, B:W.413 Hydrogen bonds: B:K.275, B:K.275, B:H.277, B:T.315, B:S.316 Salt bridges: B:R.105, B:H.277, B:H.277 Metal complexes: B:H.271

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

NA.2: 5 residues within 4Å: Chain A: T.272, T.323, T.325, K.328, D.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.330 NA.5: 5 residues within 4Å: Chain B: T.272, T.323, T.325, K.328, D.330 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.323, B:D.330

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: M.59, F.63, Y.65, K.153, G.157, K.158, L.160, S.161, D.190, W.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.153, A:K.158, A:D.190 Water bridges: A:K.153 GOL.6: 8 residues within 4Å: Chain B: M.59, F.63, Y.65, K.153, G.157, K.158, D.190, W.192 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.153, B:K.153, B:D.190 Water bridges: A:V.711

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Indole-N-Linked Hydroperoxyl Adduct of Protein-Derived Cofactor Modulating Catalase-Peroxidase Functions. Angew.Chem.Int.Ed.Engl. (2024)

Release Date

2024-10-23

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase

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