SMTL ID : 4bfl.1

Structure of natively expressed catalase HPII

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: R.125, I.126, 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, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain D: D.118 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:I.126, A:V.127, A:H.128, A:A.186, A:V.199, A:N.201, A:F.206, A:F.214, A:F.214, A:F.214, A:F.214, A:I.274, A:I.274, A:L.407, A:L.407, A:R.411, A:Y.415, A:Y.415, A:T.418 Hydrogen bonds: A:Q.419 Water bridges: A:R.165, A:A.389, A:F.391 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: 25 residues within 4Å: Chain B: R.125, I.126, V.127, H.128, R.165, G.184, F.185, V.199, G.200, N.201, F.206, A.211, 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 C: D.118 29 PLIP interactions: 29 interactions with chain B, Hydrophobic interactions: B:I.126, B:V.127, B:H.128, B:V.199, B:N.201, B:F.206, B:F.206, B:A.211, 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, B:T.418 Hydrogen bonds: B:Q.419 Water bridges: B:A.389 Salt bridges: B:R.125, B:R.125, B:R.165, B:R.422 pi-Stacking: B:H.128, B:F.214 pi-Cation interactions: B:R.411 Metal complexes: B:Y.415 HEM.5: 25 residues within 4Å: Chain B: D.118 Chain C: R.125, I.126, 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 C, Hydrophobic interactions: C:I.126, C:V.127, C:H.128, C:V.199, C:F.206, C:F.214, C:F.214, C:F.214, C:F.214, C:L.407, C:L.407, C:R.411, C:Y.415, C:T.418 Hydrogen bonds: C:Q.419 Water bridges: C:R.165, C:T.418, C:T.418 Salt bridges: C:R.125, C:R.125, C:R.165, C:R.422 pi-Stacking: C:H.128, C:F.214 Metal complexes: C:Y.415 HEM.7: 26 residues within 4Å: Chain A: I.114, D.118 Chain D: R.125, I.126, 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 29 PLIP interactions: 28 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: D:I.126, 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:I.274, D:L.407, D:L.407, D:R.411, D:Y.415, A:I.114 Hydrogen bonds: D:R.165, D:Q.419 Water bridges: D:A.186, D:T.418, D:R.422 Salt bridges: D:R.125, D:R.125, D:R.165, D:R.422 pi-Stacking: D:H.128, D:F.214 Metal complexes: D:Y.415

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain B: E.224, H.226, W.227, D.237, V.535, R.536 Chain C: P.49, T.50 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:T.50, B:R.536 Water bridges: C:T.50, B:E.224, B:E.224, B:D.237, B:R.536 EDO.4: 8 residues within 4Å: Chain B: D.70, V.71, R.435, M.451 Chain D: D.70, V.71, R.435, M.451 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.435, B:D.70, B:R.435 EDO.6: 8 residues within 4Å: Chain A: D.70, V.71, R.435, M.451 Chain C: D.70, V.71, R.435, M.451 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.70, C:R.435, A:R.435

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabrielsen, M. et al., Accidents Happen: Crystallisation of Catalase from a Mixed Protein Solution. To be Published

Release Date

2013-04-03

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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