SMTL ID : 6ztw.1 (1 other biounit)

Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

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

HDD.1: 25 residues within 4Å: Chain A: 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 D: D.118 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:R.125, A:H.128, A:V.199, A:N.201, A:F.206, A:F.206, A:A.211, A:F.214, A:F.214, A:F.214, A:F.214, A:L.407, A:L.407, A:R.411, A:Y.415, A:Y.415 Hydrogen bonds: A:Q.419 Water bridges: A:R.165 Salt bridges: A:R.125, A:R.165, A:R.422 pi-Stacking: A:H.128, A:F.206, A:F.214 pi-Cation interactions: A:R.411 Metal complexes: A:Y.415 HDD.5: 23 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, F.214, I.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 27 PLIP interactions: 26 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:R.125, B:H.128, B:V.199, B:N.201, 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 Hydrogen bonds: B:Q.419 Water bridges: B:A.186, B:A.389, B:R.422 Salt bridges: B:R.125, B:R.165, B:R.422 pi-Stacking: B:H.128, B:F.206, B:F.214 pi-Cation interactions: B:R.411 Metal complexes: B:Y.415, H2O.40 HDD.11: 23 residues within 4Å: Chain C: R.125, I.126, 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 25 PLIP interactions: 24 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:R.125, C:H.128, C:V.199, C:N.201, 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:Y.415 Hydrogen bonds: C:Q.419 Water bridges: C:R.165 Salt bridges: C:R.125, C:R.165, C:R.422 pi-Stacking: C:H.128, C:F.206, C:F.214 pi-Cation interactions: C:R.411 Metal complexes: C:Y.415, H2O.62 HDD.16: 24 residues within 4Å: 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 28 PLIP interactions: 27 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:R.125, D:H.128, D:A.186, D:V.199, D:N.201, D:F.206, D:F.206, D:F.214, D:F.214, D:F.214, D:F.214, D:L.407, D:L.407, D:R.411, D:Y.415, D:Y.415 Hydrogen bonds: D:Q.419 Water bridges: D:R.125, D:A.389 Salt bridges: D:R.125, D:R.165, D:R.422 pi-Stacking: D:H.128, D:F.206, D:F.214 pi-Cation interactions: D:R.411 Metal complexes: D:Y.415, H2O.88

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 5 residues within 4Å: Chain A: R.278, E.343, E.346, E.487, R.488 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.278, A:E.487, A:R.488 Water bridges: A:E.343, A:E.343, A:E.343, A:E.346, A:E.346, A:E.346, A:E.487, D:R.100, D:R.100 TRS.6: 7 residues within 4Å: Chain B: R.278, F.288, E.343, E.346, E.487, R.488 Ligands: EDO.8 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.278, B:R.488 Water bridges: B:R.278, B:E.343, B:E.346, B:E.346, B:E.346, C:R.100, C:R.100 TRS.12: 7 residues within 4Å: Chain C: R.278, F.288, E.343, E.346, E.487, R.488 Ligands: EDO.14 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.278, C:E.487, C:R.488 Water bridges: C:E.343, C:E.343, C:E.346, C:E.346, C:E.487, B:R.100, B:R.100 TRS.17: 6 residues within 4Å: Chain D: R.278, F.288, E.343, E.346, E.487, R.488 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.278, D:R.488 Water bridges: D:R.278, D:E.343, D:E.346, A:R.100

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: T.516, F.518, Y.591, A.592 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.592 GOL.4: 3 residues within 4Å: Chain A: P.462 Chain B: L.245, Q.246 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Q.92 GOL.10: 5 residues within 4Å: Chain B: Q.713, E.715, E.716, I.718, E.731 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.718 Water bridges: B:E.715 GOL.15: 3 residues within 4Å: Chain C: K.348, F.349, L.364 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.348 Water bridges: C:L.364

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 5 residues within 4Å: Chain B: D.345, K.348, F.349, L.364, N.580 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.345, B:K.348, B:F.349, B:F.349

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

EDO.8: 2 residues within 4Å: Chain B: Q.486 Ligands: TRS.6 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.485 EDO.9: 4 residues within 4Å: Chain B: E.430, R.435, M.451 Chain D: K.73 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:K.73, D:K.73, B:R.435 Water bridges: B:G.452 EDO.13: 4 residues within 4Å: Chain C: K.142, L.144, I.147, Q.368 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.142 EDO.14: 3 residues within 4Å: Chain C: Y.485, Q.486 Ligands: TRS.12 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.492

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grzechowiak, M. et al., Serendipitous crystallization of E. coli HPII catalase, a sequel to "the tale usually not told". Acta Biochim.Pol. (2021)

Release Date

2020-10-07

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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