SMTL ID : 2isa.1 (1 other biounit)

Crystal Structure of Vibrio salmonicida catalase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: R.50, M.52, H.53, R.90, G.109, F.110, S.111, A.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, A.335, Y.336, A.339, Q.340, R.343 Chain B: L.39, D.43 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:H.53, A:N.126, A:P.136, A:F.139, A:F.139, A:F.139, A:F.139, A:F.139, A:L.277, A:R.332, A:A.335, A:Y.336, A:A.339, B:L.39 Hydrogen bonds: A:Q.340 Water bridges: A:S.111, A:A.310, A:R.343 Salt bridges: A:R.50, A:R.90, A:R.343 pi-Stacking: A:H.53, A:F.131, A:F.139 pi-Cation interactions: A:R.332 Metal complexes: A:Y.336 HEM.4: 26 residues within 4Å: Chain A: L.39, D.43 Chain B: R.50, M.52, H.53, R.90, G.109, F.110, S.111, A.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, A.335, Y.336, A.339, Q.340, R.343 29 PLIP interactions: 28 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:H.53, B:N.126, B:P.136, B:F.139, B:F.139, B:F.139, B:F.139, B:F.139, B:L.277, B:F.312, B:R.332, B:A.335, B:Y.336, B:Y.336, B:A.339, A:L.39 Hydrogen bonds: B:S.111, B:Q.340 Water bridges: B:A.310, B:R.343 Salt bridges: B:R.50, B:R.50, B:R.90, B:R.343 pi-Stacking: B:H.53, B:F.131, B:F.139 pi-Cation interactions: B:R.332 Metal complexes: B:Y.336 HEM.6: 26 residues within 4Å: Chain C: R.50, M.52, H.53, R.90, G.109, F.110, S.111, A.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, A.335, Y.336, A.339, Q.340, R.343 Chain D: L.39, D.43 26 PLIP interactions: 25 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:H.53, C:N.126, C:P.136, C:F.139, C:F.139, C:F.139, C:F.139, C:L.277, C:R.332, C:A.335, C:Y.336, C:Y.336, C:A.339, D:L.39 Hydrogen bonds: C:S.111, C:Q.340 Water bridges: C:A.310, C:R.343 Salt bridges: C:R.50, C:R.90, C:R.343 pi-Stacking: C:H.53, C:F.131, C:F.139 pi-Cation interactions: C:R.332 Metal complexes: C:Y.336 HEM.9: 26 residues within 4Å: Chain C: L.39, D.43 Chain D: R.50, M.52, H.53, R.90, G.109, F.110, S.111, A.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, A.335, Y.336, A.339, Q.340, R.343 26 PLIP interactions: 25 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:H.53, D:N.126, D:P.136, D:F.139, D:F.139, D:F.139, D:F.139, D:L.277, D:R.332, D:A.335, D:Y.336, D:Y.336, D:A.339, C:L.39 Hydrogen bonds: D:Q.340 Water bridges: D:A.310, D:R.343 Salt bridges: D:R.50, D:R.50, D:R.90, D:R.343 pi-Stacking: D:H.53, D:F.131, D:F.139 pi-Cation interactions: D:R.332 Metal complexes: D:Y.336

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: N.313, A.315, L.333, F.334, G.337, D.338, R.341 Chain C: V.33, L.36, E.37 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.313, A:D.338, A:R.341, A:R.341 Water bridges: C:V.33 GOL.5: 10 residues within 4Å: Chain B: N.313, A.315, L.333, F.334, G.337, D.338, R.341 Chain D: V.33, L.36, E.37 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:V.33, B:N.313, B:D.338, B:R.341, B:R.341 Water bridges: D:E.37, D:E.37, D:E.37, B:Y.336 GOL.7: 10 residues within 4Å: Chain A: V.33, L.36, E.37 Chain C: N.313, A.315, L.333, F.334, G.337, D.338, R.341 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:N.313, C:G.337, C:D.338, C:R.341, C:R.341, A:E.37 Water bridges: C:Y.336, A:V.33, A:E.37, A:E.37, A:E.37 GOL.10: 10 residues within 4Å: Chain B: V.33, L.36, E.37 Chain D: N.313, A.315, L.333, F.334, G.337, D.338, R.341 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.313, D:G.337, D:D.338, D:R.341, D:R.341, B:V.33 Water bridges: D:Y.336

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

CL.3: 2 residues within 4Å: Chain B: R.44 Chain C: R.44 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: R.44 Chain D: R.44 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riise, E.K. et al., The first structure of a cold-active catalase from Vibrio salmonicida at 1.96A reveals structural aspects of cold adaptation. ACTA CRYSTALLOGR.,SECT.D (2007)

Release Date

2007-01-23

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase

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