SMTL ID : 1si8.1

Crystal structure of E. faecalis catalase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: V.14, G.15, D.16, H.35 11 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:G.15, A:D.16 Water bridges: A:P.13, A:P.13, A:D.16, A:D.16, A:L.36, D:N.409, D:N.409, C:A.396, C:I.398 SO4.2: 3 residues within 4Å: Chain A: R.182, H.192, K.216 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.182, A:H.192, A:K.216 SO4.5: 4 residues within 4Å: Chain B: V.14, G.15, D.16, H.35 6 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:G.15, B:D.16, B:D.16 Water bridges: B:H.35, D:I.398, C:N.409 SO4.6: 4 residues within 4Å: Chain B: R.182, H.192, K.216, I.221 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.216 Salt bridges: B:R.182, B:H.192, B:K.216 SO4.8: 4 residues within 4Å: Chain C: V.14, G.15, D.16, H.35 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.15, C:D.16, C:D.16 Water bridges: C:P.13, C:P.13, C:D.33, C:D.33, B:N.409 SO4.9: 3 residues within 4Å: Chain C: R.182, H.192, K.216 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.182, C:R.182 Salt bridges: C:R.182, C:H.192, C:K.216 SO4.12: 4 residues within 4Å: Chain D: V.14, G.15, D.16, H.35 8 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:P.13, D:G.15, D:D.16 Water bridges: D:D.16, D:D.33, D:L.36, B:I.398, A:N.409 SO4.13: 3 residues within 4Å: Chain D: R.182, H.192, K.216 4 PLIP interactions: 4 interactions with chain D Water bridges: D:K.216 Salt bridges: D:R.182, D:H.192, D:K.216

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

CL.3: 2 residues within 4Å: Chain A: R.45 Chain B: R.45 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain C: R.45 Chain D: R.45 Ligand excluded by PLIP

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.4: 25 residues within 4Å: Chain A: R.51, V.52, V.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, F.132, A.137, F.140, S.196, H.197, F.313, L.329, R.333, A.336, Y.337, A.340, H.341, R.344 Chain D: N.44 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:V.52, A:V.53, A:H.54, A:A.112, A:V.125, A:N.127, A:F.132, A:A.137, A:F.140, A:F.140, A:F.140, A:F.140, A:F.313, A:L.329, A:L.329, A:R.333, A:A.336, A:Y.337, A:Y.337 Water bridges: A:A.112, A:V.311, A:R.344, A:R.344 Salt bridges: A:R.51, A:R.51, A:R.91, A:H.341, A:R.344 pi-Stacking: A:H.54, A:F.140 pi-Cation interactions: A:R.333 Metal complexes: A:Y.337 HEM.7: 24 residues within 4Å: Chain B: R.51, V.52, V.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, F.132, A.137, F.140, S.196, H.197, F.313, L.329, R.333, Y.337, A.340, H.341, R.344 Chain C: N.44 32 PLIP interactions: 32 interactions with chain B, Hydrophobic interactions: B:V.52, B:V.53, B:H.54, B:A.112, B:V.125, B:N.127, B:F.132, B:A.137, B:F.140, B:F.140, B:F.140, B:F.140, B:F.313, B:L.329, B:L.329, B:L.329, B:R.333, B:Y.337, B:Y.337 Water bridges: B:A.112, B:V.311, B:R.344, B:R.344 Salt bridges: B:R.51, B:R.51, B:R.91, B:H.341, B:R.344 pi-Stacking: B:H.54, B:F.140 pi-Cation interactions: B:R.333 Metal complexes: B:Y.337 HEM.11: 26 residues within 4Å: Chain B: N.44 Chain C: R.51, V.52, V.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, F.132, A.137, F.140, G.195, S.196, H.197, F.313, L.329, R.333, A.336, Y.337, A.340, H.341, R.344 31 PLIP interactions: 31 interactions with chain C, Hydrophobic interactions: C:V.52, C:V.53, C:H.54, C:A.112, C:V.125, C:N.127, C:F.132, C:A.137, C:F.140, C:F.140, C:F.140, C:F.140, C:F.313, C:L.329, C:L.329, C:R.333, C:A.336, C:Y.337, C:Y.337 Water bridges: C:V.311, C:R.344, C:R.344 Salt bridges: C:R.51, C:R.51, C:R.91, C:H.341, C:R.344 pi-Stacking: C:H.54, C:F.140 pi-Cation interactions: C:R.333 Metal complexes: C:Y.337 HEM.14: 26 residues within 4Å: Chain A: N.44 Chain D: R.51, V.52, V.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, F.132, A.137, F.140, G.195, S.196, H.197, F.313, L.329, R.333, A.336, Y.337, A.340, H.341, R.344 31 PLIP interactions: 31 interactions with chain D, Hydrophobic interactions: D:V.52, D:V.53, D:H.54, D:A.112, D:V.125, D:N.127, D:F.132, D:A.137, D:F.140, D:F.140, D:F.140, D:F.140, D:F.313, D:L.329, D:L.329, D:R.333, D:A.336, D:Y.337, D:Y.337 Water bridges: D:A.112, D:V.311, D:R.344 Salt bridges: D:R.51, D:R.51, D:R.91, D:H.341, D:R.344 pi-Stacking: D:H.54, D:F.140 pi-Cation interactions: D:R.333 Metal complexes: D:Y.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hakansson, K.O. et al., The three-dimensional structure of catalase from Enterococcus faecalis. Acta Crystallogr.,Sect.D (2004)

Release Date

2004-05-04

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase