SMTL ID : 6by0.1

Crystal structure of catalase HPII from E. coli in space group P1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: R.125, V.127, H.128, R.165, G.184, F.185, V.199, G.200, N.201, F.206, F.214, I.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain B: D.118 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:R.125, A:V.127, A:H.128, A:V.199, A:F.206, A:F.214, A:F.214, A:F.214, A:F.214, A:I.274, A:F.391, A:L.407, A:R.411, A:Y.415, A:Y.415, A:Y.415 Hydrogen bonds: A:F.391, A:Q.419 Water bridges: A:R.165 Salt bridges: A:R.125, A:R.125, A:R.165, A:R.422 pi-Stacking: A:H.128, A:F.214 Metal complexes: A:Y.415 HEM.2: 23 residues within 4Å: Chain A: I.114, D.118 Chain B: R.125, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, F.214, I.274, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 27 PLIP interactions: 26 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:H.128, B:A.186, B:V.199, B:N.201, B:F.206, B:F.206, B:F.214, B:F.214, B:F.214, B:F.214, B:L.407, B:L.407, B:R.411, B:Y.415, B:Y.415, B:Y.415, A:I.114 Hydrogen bonds: B:R.165, B:F.391, B:Q.419 Water bridges: B:A.186 Salt bridges: B:R.125, B:R.165, B:R.422 pi-Stacking: B:H.128, B:F.214 Metal complexes: B:Y.415 HEM.3: 23 residues within 4Å: Chain C: R.125, V.127, H.128, R.165, G.184, F.185, V.199, G.200, N.201, F.206, F.214, I.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain D: D.118 24 PLIP interactions: 24 interactions with chain C, Hydrophobic interactions: C:H.128, C:V.199, C:N.201, C:F.206, C:F.206, C:F.214, C:F.214, C:F.214, C:F.214, C:I.274, C:L.407, C:L.407, C:R.411, C:Y.415, C:Y.415, C:Y.415 Hydrogen bonds: C:T.418, C:Q.419 Salt bridges: C:R.125, C:R.165, C:R.422 pi-Stacking: C:H.128, C:F.214 Metal complexes: C:Y.415 HEM.4: 24 residues within 4Å: Chain C: D.118 Chain D: R.125, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, F.214, I.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 25 PLIP interactions: 25 interactions with chain D, Hydrophobic interactions: D:V.127, D:H.128, D:A.186, D:V.199, D:F.206, D:F.214, D:F.214, D:F.214, D:F.214, D:I.274, D:L.407, D:L.407, D:R.411, D:Y.415, D:Y.415 Hydrogen bonds: D:F.391, D:Q.419 Water bridges: D:R.165, D:R.165 Salt bridges: D:R.125, D:R.165, D:R.422 pi-Stacking: D:H.128, D:F.214 Metal complexes: D:Y.415

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Simpkin, A.J. et al., SIMBAD: a sequence-independent molecular-replacement pipeline. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-01-24

Peptides

Catalase HPII: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase HPII

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