SMTL ID : 1sy7.1

Crystal structure of the catalase-1 from Neurospora crassa, native structure at 1.75A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x HDD: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE(Non-covalent)

HDD.1: 28 residues within 4Å: Chain A: R.68, V.69, V.70, H.71, R.108, G.127, F.128, A.129, V.142, G.143, N.144, F.149, A.154, F.157, V.217, N.218, F.334, L.350, G.353, R.354, S.357, Y.358, T.361, Q.362, R.365 Chain C: F.60, D.61 Ligands: HEM.2 31 PLIP interactions: 30 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:R.68, A:H.71, A:A.129, A:V.142, A:N.144, A:F.149, A:A.154, A:F.157, A:F.157, A:F.157, A:F.157, A:V.217, A:V.217, A:F.334, A:L.350, A:L.350, A:R.354, A:Y.358, A:T.361, C:F.60 Hydrogen bonds: A:Q.362 Water bridges: A:R.108, A:R.365, A:R.365 Salt bridges: A:R.68, A:R.108, A:R.365 pi-Stacking: A:H.71, A:F.157 pi-Cation interactions: A:R.354 Metal complexes: A:Y.358 HDD.3: 28 residues within 4Å: Chain B: R.68, V.69, V.70, H.71, R.108, G.127, F.128, A.129, V.142, G.143, N.144, F.149, A.154, F.157, V.217, N.218, F.334, L.350, G.353, R.354, S.357, Y.358, T.361, Q.362, R.365 Chain D: F.60, D.61 Ligands: HEM.4 31 PLIP interactions: 30 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:R.68, B:H.71, B:A.129, B:V.142, B:N.144, B:F.149, B:A.154, B:F.157, B:F.157, B:F.157, B:F.157, B:V.217, B:V.217, B:F.334, B:L.350, B:L.350, B:R.354, B:Y.358, B:T.361, D:F.60 Hydrogen bonds: B:Q.362 Water bridges: B:R.108, B:R.365, B:R.365 Salt bridges: B:R.68, B:R.108, B:R.365 pi-Stacking: B:H.71, B:F.157 pi-Cation interactions: B:R.354 Metal complexes: B:Y.358 HDD.5: 28 residues within 4Å: Chain A: F.60, D.61 Chain C: R.68, V.69, V.70, H.71, R.108, G.127, F.128, A.129, V.142, G.143, N.144, F.149, A.154, F.157, V.217, N.218, F.334, L.350, G.353, R.354, S.357, Y.358, T.361, Q.362, R.365 Ligands: HEM.6 31 PLIP interactions: 30 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:R.68, C:H.71, C:A.129, C:V.142, C:N.144, C:F.149, C:A.154, C:F.157, C:F.157, C:F.157, C:F.157, C:V.217, C:V.217, C:F.334, C:L.350, C:L.350, C:R.354, C:Y.358, C:T.361, A:F.60 Hydrogen bonds: C:Q.362 Water bridges: C:R.108, C:R.365, C:R.365 Salt bridges: C:R.68, C:R.108, C:R.365 pi-Stacking: C:H.71, C:F.157 pi-Cation interactions: C:R.354 Metal complexes: C:Y.358 HDD.7: 28 residues within 4Å: Chain B: F.60, D.61 Chain D: R.68, V.69, V.70, H.71, R.108, G.127, F.128, A.129, V.142, G.143, N.144, F.149, A.154, F.157, V.217, N.218, F.334, L.350, G.353, R.354, S.357, Y.358, T.361, Q.362, R.365 Ligands: HEM.8 31 PLIP interactions: 30 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:R.68, D:H.71, D:A.129, D:V.142, D:N.144, D:F.149, D:A.154, D:F.157, D:F.157, D:F.157, D:F.157, D:V.217, D:V.217, D:F.334, D:L.350, D:L.350, D:R.354, D:Y.358, D:T.361, B:F.60 Hydrogen bonds: D:Q.362 Water bridges: D:R.108, D:R.365, D:R.365 Salt bridges: D:R.68, D:R.108, D:R.365 pi-Stacking: D:H.71, D:F.157 pi-Cation interactions: D:R.354 Metal complexes: D:Y.358

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

HEM.2: 27 residues within 4Å: Chain A: R.68, V.69, V.70, H.71, R.108, G.127, F.128, A.129, V.142, G.143, N.144, F.149, A.154, F.157, V.217, N.218, F.334, L.350, R.354, S.357, Y.358, T.361, Q.362, R.365 Chain C: I.57, D.61 Ligands: HDD.1 32 PLIP interactions: 31 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:V.69, A:H.71, A:A.129, A:V.142, A:N.144, A:F.149, A:A.154, A:F.157, A:F.157, A:F.157, A:F.157, A:V.217, A:V.217, A:F.334, A:L.350, A:L.350, A:R.354, A:T.361, C:I.57 Hydrogen bonds: A:Q.362 Water bridges: A:V.69, A:I.332, A:T.361, A:R.365 Salt bridges: A:R.68, A:R.68, A:R.108, A:R.365 pi-Stacking: A:H.71, A:F.157 pi-Cation interactions: A:R.354 Metal complexes: A:Y.358 HEM.4: 27 residues within 4Å: Chain B: R.68, V.69, V.70, H.71, R.108, G.127, F.128, A.129, V.142, G.143, N.144, F.149, A.154, F.157, V.217, N.218, F.334, L.350, R.354, S.357, Y.358, T.361, Q.362, R.365 Chain D: I.57, D.61 Ligands: HDD.3 32 PLIP interactions: 31 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:V.69, B:H.71, B:A.129, B:V.142, B:N.144, B:F.149, B:A.154, B:F.157, B:F.157, B:F.157, B:F.157, B:V.217, B:V.217, B:F.334, B:L.350, B:L.350, B:R.354, B:T.361, D:I.57 Hydrogen bonds: B:Q.362 Water bridges: B:E.67, B:V.69, B:I.332, B:R.365 Salt bridges: B:R.68, B:R.68, B:R.108, B:R.365 pi-Stacking: B:H.71, B:F.157 pi-Cation interactions: B:R.354 Metal complexes: B:Y.358 HEM.6: 27 residues within 4Å: Chain A: I.57, D.61 Chain C: R.68, V.69, V.70, H.71, R.108, G.127, F.128, A.129, V.142, G.143, N.144, F.149, A.154, F.157, V.217, N.218, F.334, L.350, R.354, S.357, Y.358, T.361, Q.362, R.365 Ligands: HDD.5 32 PLIP interactions: 31 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:V.69, C:H.71, C:A.129, C:V.142, C:N.144, C:F.149, C:A.154, C:F.157, C:F.157, C:F.157, C:F.157, C:V.217, C:V.217, C:F.334, C:L.350, C:L.350, C:R.354, C:T.361, A:I.57 Hydrogen bonds: C:Q.362 Water bridges: C:V.69, C:I.332, C:T.361, C:R.365 Salt bridges: C:R.68, C:R.68, C:R.108, C:R.365 pi-Stacking: C:H.71, C:F.157 pi-Cation interactions: C:R.354 Metal complexes: C:Y.358 HEM.8: 27 residues within 4Å: Chain B: I.57, D.61 Chain D: R.68, V.69, V.70, H.71, R.108, G.127, F.128, A.129, V.142, G.143, N.144, F.149, A.154, F.157, V.217, N.218, F.334, L.350, R.354, S.357, Y.358, T.361, Q.362, R.365 Ligands: HDD.7 32 PLIP interactions: 31 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:V.69, D:H.71, D:A.129, D:V.142, D:N.144, D:F.149, D:A.154, D:F.157, D:F.157, D:F.157, D:F.157, D:V.217, D:V.217, D:F.334, D:L.350, D:L.350, D:R.354, D:T.361, B:I.57 Hydrogen bonds: D:Q.362 Water bridges: D:E.67, D:V.69, D:I.332, D:R.365 Salt bridges: D:R.68, D:R.68, D:R.108, D:R.365 pi-Stacking: D:H.71, D:F.157 pi-Cation interactions: D:R.354 Metal complexes: D:Y.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz, A. et al., Unusual Cys-Tyr covalent bond in a large catalase. J.Mol.Biol. (2004)

Release Date

2004-10-12

Peptides

Catalase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Catalase 1