SMTL ID : 8u3p.1 (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.323 NA.8: 4 residues within 4Å: Chain B: T.272, T.323, T.325, K.328 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.323, B:D.330

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE

HEM.2: 26 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, I.318, W.322, L.379, T.381, F.409, W.413 33 PLIP interactions: 32 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.104, 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: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: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.9: 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 29 PLIP interactions: 28 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:I.104, B:R.105, B:W.108, B:W.108, B:W.108, B:P.233, 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:H.277 Salt bridges: B:R.105, B:H.277, B:H.277 pi-Stacking: B:W.108 Metal complexes: B:H.271, H2O.49

2 x ACT: ACETATE ION

ACT.3: 4 residues within 4Å: Chain A: G.178, F.179, K.180, A.406 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.180 Water bridges: A:W.329 ACT.10: 9 residues within 4Å: Chain A: M.59, G.157, K.158 Chain B: V.711, A.714, D.716, A.717, K.720 Ligands: GOL.4 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.711, B:A.717, B:K.720 Salt bridges: A:K.153

10 x GOL: GLYCEROL

GOL.4: 10 residues within 4Å: Chain A: M.59, F.63, Y.65, K.153, G.157, K.158, L.160, S.161, D.190 Ligands: ACT.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.153, A:K.158, A:D.190 GOL.5: 7 residues within 4Å: Chain A: R.43, L.44, E.608, Y.609, R.694, V.698, N.702 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.44, A:Y.609, A:R.694, A:N.702 GOL.6: 3 residues within 4Å: Chain A: N.259, E.408, K.411 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.259, A:N.259, A:E.408, A:K.411 Water bridges: A:K.411 GOL.7: 9 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:H.117, A:R.485, A:K.614 Water bridges: A:K.591, A:A.592 GOL.11: 10 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 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.153, B:K.158, B:D.190 Water bridges: B:K.153, A:D.716 GOL.12: 7 residues within 4Å: Chain B: H.117, R.485, V.587, L.588, P.590, K.614, L.617 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.117, B:R.485, B:K.614, B:K.614 Water bridges: B:K.591, B:A.592 GOL.13: 8 residues within 4Å: Chain A: P.289, E.290, A.292, P.293, L.294 Chain B: S.701, N.702 Ligands: GOL.14 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:P.289, B:S.701, B:S.701 Water bridges: A:G.298, B:N.702, B:S.703, B:S.703 GOL.14: 8 residues within 4Å: Chain B: R.43, L.44, E.608, Y.609, R.694, V.698, N.702 Ligands: GOL.13 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.44, B:E.608, B:E.608, B:Y.609, B:R.694, B:N.702 Water bridges: A:E.290 GOL.15: 8 residues within 4Å: Chain B: V.48, L.49, H.50, Q.51, A.615, N.616, T.619, L.620 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.49, B:Q.51, B:N.616, B:N.616, B:L.620 GOL.16: 6 residues within 4Å: Chain B: I.116, H.117, N.219, R.254, R.255, V.587 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.117, B:R.254, B:R.254 Water bridges: B:P.220, B:L.221

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
A

B
D

Catalase-peroxidase

Related Entries With Identical Sequence