SMTL ID : 8w1w.2 (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: 25 residues within 4Å: Chain A: P.101, L.102, I.104, R.105, X.108, V.231, P.233, I.249, L.266, I.267, G.270, H.271, F.273, G.274, K.275, T.276, H.277, T.315, S.316, I.318, W.322, L.379, T.381, F.409, W.413 28 PLIP interactions: 28 interactions with chain A, Hydrophobic interactions: A:I.104, A:R.105, A:P.233, A:I.249, A:L.266, A:I.267, A:I.267, A:T.276, A:I.318, A:W.322, 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:R.105, A:H.277 Salt bridges: A:R.105, A:H.277, A:H.277 Metal complexes: A:H.271 HEM.8: 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:P.233, B:I.249, B:F.253, B:L.266, B:I.267, B:T.276, B:W.322, B:W.322, B:L.379, B:T.381, 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: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: 4 residues within 4Å: Chain A: T.272, T.323, T.325, K.328 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.328 Water bridges: A:D.330 NA.9: 5 residues within 4Å: Chain B: T.272, T.323, T.325, P.326, K.328 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.323, B:T.325

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: M.59, F.63, Y.65, K.153, G.157, K.158, L.160, S.161, D.190 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.153, A:K.158, A:D.190 Water bridges: A:K.158, B:V.711 GOL.4: 7 residues within 4Å: Chain A: H.117, R.485, V.587, E.589, P.590, K.614, L.617 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.117, A:R.485, A:K.614, A:K.614 Water bridges: A:A.592 GOL.5: 4 residues within 4Å: Chain A: N.259, E.262, E.408, K.411 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.259, A:N.259, A:K.411 GOL.10: 9 residues within 4Å: Chain B: M.59, F.63, Y.65, K.153, G.157, K.158, L.160, S.161, D.190 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.153, B:K.158, B:D.190, B:D.190 GOL.11: 6 residues within 4Å: Chain A: P.289, E.290, A.292, L.294 Chain B: S.701, N.702 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:A.292, B:S.701, B:S.701 Water bridges: A:G.298, B:N.702, B:S.703, B:S.703 GOL.12: 7 residues within 4Å: Chain B: R.120, D.195, G.486, S.487, N.616, L.617, T.619 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.120, B:L.617

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

ACT.6: 5 residues within 4Å: Chain A: R.43, L.44, E.608, V.698, N.702 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.44, A:N.702 ACT.7: 4 residues within 4Å: Chain A: G.178, F.179, K.180, A.406 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.180 Water bridges: A:K.180

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
B

B
C

Catalase-peroxidase

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