SMTL ID : 8w1x.1

2.35-angstrom resolution intermediate crystal structure of KatG from Mycobacterium tuberculosis with an MYW-OOH cofactor soaked with peroxide for 5 minutes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-mer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: P.101, L.102, R.105, W.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 Ligands: OXY.2 27 PLIP interactions: 26 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:R.105, A:W.108, A:W.108, A:W.108, A:P.233, A:I.249, A:F.253, A:L.266, A:I.267, A:T.276, A:W.322, A:L.379, A:T.381, A:W.413 Hydrogen bonds: A:K.275, A:H.277, A:S.316 Water bridges: A:R.105, A:R.105, A:H.277 Salt bridges: A:R.105, A:H.277, A:H.277 pi-Stacking: A:W.108 pi-Cation interactions: A:H.271 Metal complexes: A:H.271, H2O.2 HEM.5: 22 residues within 4Å: Chain B: P.101, L.102, I.104, R.105, X.108, V.231, P.233, F.253, L.266, I.267, G.270, H.271, G.274, K.275, T.276, H.277, T.315, S.316, W.322, L.379, T.381, W.413 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:I.104, B:R.105, B:V.231, B:P.233, B:F.253, B:L.266, B:I.267, B:T.276, B:W.322, B:L.379, B:W.413 Hydrogen bonds: B:K.275, B:H.277, B:T.315, B:S.316 Water bridges: B:R.105, B:R.105, B:R.105 Salt bridges: B:R.105, B:H.277, B:H.277 Metal complexes: B:H.271

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 4 residues within 4Å: Chain A: R.105, H.109, D.138 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.105

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

NA.3: 5 residues within 4Å: Chain A: T.272, T.323, T.325, K.328, D.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.325, A:T.325

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

ACT.4: 8 residues within 4Å: Chain A: V.48, L.49, H.50, Q.51, N.616, T.619, L.620, S.621 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.51, A:N.616 ACT.8: 7 residues within 4Å: Chain B: V.48, L.49, H.50, Q.51, N.616, T.619, L.620 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.51, B:N.616, B:N.616

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain B: F.63, Y.65, K.153, G.157, K.158, L.160, S.161, D.190, W.192 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.153, B:K.158, B:D.190, B:D.190 Water bridges: B:R.129 GOL.7: 6 residues within 4Å: Chain A: P.289, E.290, A.292, L.294 Chain B: S.701, N.702 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.701 Water bridges: B:N.702, B:S.703, B:S.703, A:P.289, A:G.298

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: A
Catalase-peroxidase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase

Catalase-peroxidase

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