SMTL ID : 8u3p.2 (1 other biounit)

1.79 Angstrom resolution crystal structure of KatG from Mycobacterium tuberculosis with an MYW cofactor after heat incubation for 60 minutes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

2 x NA: SODIUM ION

NA.1: 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:T.325 NA.10: 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

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE

HEM.2: 25 residues within 4Å: Chain A: P.101, L.102, I.104, 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, F.409, W.413 29 PLIP interactions: 28 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.104, A:R.105, 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:W.322, A:L.379, 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:R.105, A:S.141, A:H.277 Salt bridges: A:R.105, A:H.277, A:H.277 pi-Stacking: A:W.108 Metal complexes: A:H.271, H2O.9 HEM.11: 25 residues within 4Å: Chain B: P.101, L.102, I.104, 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, F.409, W.413 26 PLIP interactions: 25 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:I.104, B:R.105, B:W.108, B:W.108, B:P.233, B:I.249, B:F.253, B:L.266, B:I.267, B:T.276, 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:H.277 Salt bridges: B:R.105, B:H.277, B:H.277 pi-Stacking: B:W.108 Metal complexes: B:H.271, H2O.47

2 x ACT: ACETATE ION

ACT.3: 7 residues within 4Å: Chain A: V.711, A.714, D.716 Chain B: M.59, G.157, K.158 Ligands: GOL.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.711 Hydrogen bonds: A:D.716 Salt bridges: B:K.153 ACT.4: 4 residues within 4Å: Chain A: G.178, F.179, K.180, A.406 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.180

7 x GOL: GLYCEROL

GOL.5: 7 residues within 4Å: Chain A: H.117, D.118, R.485, V.587, 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 Water bridges: A:K.591, A:A.592 GOL.6: 8 residues within 4Å: Chain A: F.63, Y.65, K.153, G.157, K.158, L.160, D.190, W.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.153, A:G.157, A:D.190 GOL.7: 7 residues within 4Å: Chain A: R.43, L.44, E.608, Y.609, V.698, N.702 Ligands: GOL.9 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Water bridges: B:E.290, A:R.694, A:R.694, A:S.703 Hydrogen bonds: A:L.44, A:E.608, A:N.702 GOL.8: 5 residues within 4Å: Chain A: P.671, G.677, T.678, Y.679, R.694 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.677, A:T.678, A:Y.679, A:R.694 GOL.9: 7 residues within 4Å: Chain A: S.701, N.702 Chain B: P.289, E.290, A.292, L.294 Ligands: GOL.7 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:P.289, B:E.290 Water bridges: B:G.298, A:S.703, A:S.703 GOL.12: 11 residues within 4Å: Chain B: M.59, F.63, Y.65, K.153, G.157, K.158, L.160, S.161, D.190, W.192 Ligands: ACT.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.153, B:K.158, B:D.190 Water bridges: B:K.153 GOL.13: 9 residues within 4Å: Chain B: H.117, D.118, R.485, V.587, L.588, E.589, P.590, K.614, L.617 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.117, B:R.485, B:K.614 Water bridges: B:K.591, B:A.592

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

2024-09-11

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Catalase-peroxidase

Related Entries With Identical Sequence