SMTL ID : 6rjn.1

Crystal structure of a Fungal Catalase at 2.3 Angstroms

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: R.65, V.66, V.67, H.68, R.105, G.124, F.125, S.126, V.139, Y.140, N.141, F.154, S.209, H.211, L.292, F.327, V.343, S.346, R.347, S.350, Y.351, T.354, H.355, R.358 Chain D: D.58 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:V.66, A:V.67, A:H.68, A:V.139, A:N.141, A:F.154, A:F.154, A:F.154, A:F.154, A:F.154, A:L.292, A:V.343, A:R.347, A:Y.351, A:Y.351, A:T.354 Water bridges: A:V.66, A:S.126, A:A.325, A:R.358 Salt bridges: A:R.65, A:R.65, A:R.105, A:H.355, A:R.358 pi-Stacking: A:H.68, A:F.146, A:F.154 pi-Cation interactions: A:R.347 Metal complexes: A:Y.351 HEM.14: 25 residues within 4Å: Chain B: R.65, V.66, V.67, H.68, R.105, G.124, F.125, S.126, V.139, Y.140, N.141, F.154, S.209, H.211, L.292, F.327, V.343, S.346, R.347, S.350, Y.351, T.354, H.355, R.358 Chain C: D.58 31 PLIP interactions: 31 interactions with chain B, Hydrophobic interactions: B:V.66, B:V.67, B:H.68, B:V.139, B:N.141, B:F.154, B:F.154, B:F.154, B:F.154, B:F.154, B:L.292, B:V.343, B:R.347, B:Y.351, B:Y.351, B:T.354 Hydrogen bonds: B:S.126 Water bridges: B:V.66, B:S.126, B:F.327, B:R.358 Salt bridges: B:R.65, B:R.65, B:R.105, B:H.355, B:R.358 pi-Stacking: B:H.68, B:F.146, B:F.154 pi-Cation interactions: B:R.347 Metal complexes: B:Y.351 HEM.26: 26 residues within 4Å: Chain B: D.58 Chain C: R.65, V.66, V.67, H.68, R.105, G.124, F.125, S.126, V.139, Y.140, N.141, P.151, F.154, S.209, H.211, L.292, F.327, V.343, S.346, R.347, S.350, Y.351, T.354, H.355, R.358 30 PLIP interactions: 30 interactions with chain C, Hydrophobic interactions: C:V.66, C:V.67, C:H.68, C:V.139, C:N.141, C:F.154, C:F.154, C:F.154, C:F.154, C:F.154, C:L.292, C:F.327, C:V.343, C:R.347, C:Y.351, C:Y.351, C:T.354 Water bridges: C:A.325, C:T.354, C:R.358 Salt bridges: C:R.65, C:R.65, C:R.105, C:H.355, C:R.358 pi-Stacking: C:H.68, C:F.146, C:F.154 pi-Cation interactions: C:R.347 Metal complexes: C:Y.351 HEM.40: 27 residues within 4Å: Chain A: L.54, D.58 Chain D: R.65, V.66, V.67, H.68, R.105, G.124, F.125, S.126, V.139, Y.140, N.141, P.151, F.154, S.209, H.211, L.292, F.327, V.343, S.346, R.347, S.350, Y.351, T.354, H.355, R.358 30 PLIP interactions: 1 interactions with chain A, 29 interactions with chain D, Hydrophobic interactions: A:L.54, D:V.66, D:V.67, D:H.68, D:V.139, D:N.141, D:F.154, D:F.154, D:F.154, D:F.154, D:F.154, D:L.292, D:V.343, D:R.347, D:Y.351, D:Y.351, D:T.354 Water bridges: D:V.66, D:F.327, D:R.358 Salt bridges: D:R.65, D:R.65, D:R.105, D:H.355, D:R.358 pi-Stacking: D:H.68, D:F.146, D:F.154 pi-Cation interactions: D:R.347 Metal complexes: D:Y.351

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 19 residues within 4Å: Chain A: P.144, H.187, Y.191, S.194, R.196, N.206, Y.208, H.228, K.230, V.295, W.296, P.297, H.298, Q.443, A.446, L.447, V.450, F.451, Q.457 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:P.144, A:V.295 Hydrogen bonds: A:H.187, A:S.194, A:N.206, A:Y.208, A:W.296, A:H.298, A:Q.457 Water bridges: A:R.196, A:R.196, A:R.196, A:H.228, A:K.230, A:Q.275, A:K.299, A:K.299 Salt bridges: A:R.196, A:K.230, A:H.298, A:H.298 NDP.15: 20 residues within 4Å: Chain B: P.144, H.187, Y.191, S.194, R.196, N.206, Y.208, H.228, K.230, V.295, W.296, P.297, H.298, Q.443, A.446, L.447, V.450, F.451, Q.457 Ligands: GOL.19 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:P.144, B:V.295 Hydrogen bonds: B:H.187, B:S.194, B:N.206, B:Y.208, B:W.296, B:H.298, B:H.298, B:Q.457 Water bridges: B:R.196, B:R.196, B:R.196, B:K.230, B:Q.275, B:W.296, B:H.298, B:K.299, B:K.299 Salt bridges: B:R.196, B:K.230, B:H.298, B:H.298, B:K.453 NDP.27: 20 residues within 4Å: Chain C: P.144, H.187, Y.191, S.194, R.196, N.206, Y.208, H.228, K.230, V.295, W.296, P.297, H.298, Q.443, A.446, L.447, V.450, F.451, K.453, Q.457 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:P.144 Hydrogen bonds: C:H.187, C:S.194, C:N.206, C:Y.208, C:W.296, C:H.298, C:H.298, C:Q.457 Water bridges: C:K.230, C:K.230, C:N.237, C:W.296, C:K.299, C:K.299 Salt bridges: C:R.196, C:K.230, C:H.298, C:H.298, C:H.298, C:K.453 pi-Cation interactions: C:R.196, C:R.196 NDP.41: 20 residues within 4Å: Chain D: P.144, H.187, Y.191, S.194, R.196, N.206, Y.208, H.228, K.230, V.295, W.296, P.297, H.298, Q.443, A.446, L.447, V.450, F.451, K.453, Q.457 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:P.144, D:V.295 Hydrogen bonds: D:H.187, D:S.194, D:N.206, D:Y.208, D:Y.208, D:W.296, D:H.298, D:Q.457, D:Q.457 Water bridges: D:R.196, D:R.196, D:H.228, D:K.230, D:K.230, D:Q.275, D:K.299, D:K.299 Salt bridges: D:R.196, D:K.230, D:H.298, D:H.298, D:H.298, D:K.453 pi-Cation interactions: D:R.196, D:R.196

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: W.448, K.449, Y.488, E.490 Ligand excluded by PLIP GOL.4: 2 residues within 4Å: Chain A: C.370, N.388 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: E.24, Q.46 Chain B: K.214, Y.216, Q.337, E.418 Chain D: T.425 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: K.214, Y.216, Q.337, P.338, E.418 Chain B: E.24, Q.46 Chain C: T.425 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: A.119, R.120, N.240, A.243, G.244 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: D.171, N.173 Chain D: F.401 Ligands: GOL.42 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: D.195, N.237, F.238, N.239, E.242, Q.457 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: P.297, Q.443, A.446 Ligands: NDP.15 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain B: G.114, A.247, P.251 Chain C: G.114, S.115, A.116, A.247, P.251 Ligand excluded by PLIP GOL.29: 9 residues within 4Å: Chain C: P.378, T.394, P.395, Y.397, K.398, S.399, C.402, F.404 Chain D: W.9 Ligand excluded by PLIP GOL.30: 3 residues within 4Å: Chain C: N.460, H.463, E.498 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain C: A.119, R.120, N.240, A.243, G.244 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain C: Q.364, Q.365, C.370, P.371, N.388 Ligand excluded by PLIP GOL.37: 8 residues within 4Å: Chain A: R.149, K.294, W.430, D.440 Chain D: N.35, A.37, P.38 Ligands: SO4.8 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain A: G.114, A.247, P.251 Chain D: G.114, A.116, A.247, P.251 Ligand excluded by PLIP GOL.39: 8 residues within 4Å: Chain C: H.56 Chain D: N.362, Q.365, T.377, M.380, N.388, N.390, L.391 Ligand excluded by PLIP GOL.42: 4 residues within 4Å: Chain D: S.393, P.395, F.401 Ligands: GOL.17 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 5 residues within 4Å: Chain A: Q.365, T.377, M.380, N.388, N.390 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.377, A:M.380, A:N.388 Water bridges: A:T.377, A:T.377, A:D.382, A:D.382 SO4.8: 7 residues within 4Å: Chain A: R.149, F.428, H.429, W.430, G.431, L.434 Ligands: GOL.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.431 Salt bridges: A:R.149

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 2 residues within 4Å: Chain A: R.59 Chain C: R.59 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: G.456, Q.458, R.459 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: R.59 Chain D: R.59 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: G.456, Q.458, R.459 Ligand excluded by PLIP CL.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

7 x K: POTASSIUM ION(Non-covalent)

K.11: 4 residues within 4Å: Chain A: P.144, G.210, Q.226, K.294 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:P.144, A:G.210, A:K.294, H2O.4, H2O.7 K.13: 5 residues within 4Å: Chain A: Q.379, M.380 Chain B: S.53, F.57 Chain C: P.155 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:S.53, A:Q.379, H2O.17 K.23: 4 residues within 4Å: Chain B: P.144, G.210, Q.226, K.294 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:P.144, B:G.210, B:K.294, H2O.14, H2O.16 K.25: 3 residues within 4Å: Chain B: S.53 Chain C: S.152, H.156 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:S.152, B:S.53, H2O.22, H2O.28 K.34: 4 residues within 4Å: Chain C: P.144, G.210, Q.226, K.294 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:P.144, C:G.210, C:K.294, H2O.27, H2O.31 K.36: 6 residues within 4Å: Chain B: P.155 Chain C: S.53, F.57, E.60 Chain D: Q.379, M.380 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Q.379, H2O.27 K.44: 4 residues within 4Å: Chain D: P.144, G.210, Q.226, K.294 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:P.144, D:G.210, D:K.294, H2O.39, H2O.41

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

NA.12: 4 residues within 4Å: Chain A: N.30, N.36, A.37, P.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.30, A:P.38 Water bridges: A:N.30 NA.24: 3 residues within 4Å: Chain B: N.30, N.36, P.38 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.30, B:N.36 Water bridges: B:N.30, B:K.39 NA.35: 3 residues within 4Å: Chain C: N.30, N.36, P.38 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.30, C:N.36 Water bridges: C:A.31, C:K.39 NA.45: 5 residues within 4Å: Chain D: N.30, N.36, A.37, P.38, K.39 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.30, D:A.37, D:K.39

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.20: 5 residues within 4Å: Chain B: Q.281, K.284, Q.285, D.300, F.301 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.281, B:K.284, B:Q.285 PEG.33: 2 residues within 4Å: Chain C: Q.281, Q.285 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.281, C:Q.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gomez, S. et al., Peroxisomal catalases from the yeasts Pichia pastoris and Kluyveromyces lactis as models for oxidative damage in higher eukaryotes. Free Radic. Biol. Med. (2019)

Release Date

2020-03-04

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase