SMTL ID : 8w1w.1 (1 other biounit)

2.03 angstrom resolution crystal structure of as-isolated KatG from Mycobacterium tuberculosis with an MYW-OOH cofactor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 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, I.104, 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, W.413 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:I.104, A:R.105, A:P.233, A:P.233, A:I.249, A:F.253, A:L.266, A:I.267, A:T.276, A:W.322, A:W.322, A:L.379, A:W.413 Hydrogen bonds: A:K.275, A:H.277, A:S.316 Water bridges: A:D.95, A:D.95, A:R.105, A:H.277 Salt bridges: A:R.105, A:H.277, A:H.277 Metal complexes: A:H.271 HEM.6: 25 residues within 4Å: Chain B: P.101, L.102, I.104, 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 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:I.104, B:R.105, B:I.249, B:F.253, B:L.266, B:I.267, B:I.267, B:T.276, B:W.322, B:W.322, B:L.379, B:F.409, B:W.413 Hydrogen bonds: B:K.275, B:H.277, B:T.315, B:S.316 Water bridges: B:R.105, B:S.141, B:H.277 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.7: 5 residues within 4Å: Chain B: T.272, T.323, T.325, K.328, D.330 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.323, B:T.325, B:T.325

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: F.63, Y.65, K.153, G.157, K.158, S.161, D.190, W.192 Chain B: V.711 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.153 Water bridges: A:R.129, A:W.162 GOL.4: 6 residues within 4Å: Chain A: P.289, E.290, A.292, L.294 Chain B: S.701, N.702 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:P.289, B:S.701, B:S.701 Water bridges: A:G.298, B:S.703, B:S.703 GOL.8: 9 residues within 4Å: Chain B: M.59, F.63, Y.65, K.153, G.157, K.158, S.161, D.190, W.192 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.153, B:D.190, B:D.190 GOL.9: 6 residues within 4Å: Chain B: R.120, D.195, G.486, S.487, N.616, L.617 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.120, B:R.120, B:D.195, B:G.486, B:L.617 Water bridges: B:N.616

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 3 residues within 4Å: Chain A: N.259, E.408, K.411 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.411 ACT.10: 6 residues within 4Å: Chain A: S.701, N.702 Chain B: P.289, E.290, A.292, L.294 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.701, B:A.292 Water bridges: A:S.703

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
D

Catalase-peroxidase

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