SMTL ID : 2iqf.1

Crystal structure of Helicobacter pylori catalase compound I

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-tetramer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: R.344, Y.345 Chain B: R.344, Y.345 Chain C: R.47 Chain D: R.47 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain A Salt bridges: D:R.47, C:R.47 Hydrophobic interactions: A:Y.345 ACT.6: 6 residues within 4Å: Chain A: R.47 Chain B: R.47 Chain C: R.344, Y.345 Chain D: R.344, Y.345 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Salt bridges: B:R.47, A:R.47 Hydrophobic interactions: C:Y.345

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

HEM.2: 28 residues within 4Å: Chain A: R.53, V.54, V.55, H.56, R.93, G.112, F.113, A.114, V.127, G.128, N.129, F.134, A.139, F.142, G.197, S.198, H.199, F.315, M.331, R.335, S.338, Y.339, T.342, H.343, R.346 Chain C: L.42, D.46 Ligands: O.3 32 PLIP interactions: 30 interactions with chain A, 1 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: A:V.54, A:V.55, A:H.56, A:V.127, A:N.129, A:F.134, A:A.139, A:F.142, A:F.142, A:F.142, A:F.142, A:R.335, A:Y.339, A:Y.339, A:T.342, C:L.42 Water bridges: A:A.114, A:A.313, A:T.342, A:T.342, A:R.346 Salt bridges: A:R.53, A:R.53, A:R.93, A:H.343, A:R.346 pi-Stacking: A:H.56, A:F.134, A:F.142 pi-Cation interactions: A:R.335 Metal complexes: A:Y.339, O.3 HEM.4: 27 residues within 4Å: Chain B: R.53, V.54, V.55, H.56, R.93, G.112, F.113, A.114, V.127, G.128, N.129, A.139, F.142, G.197, S.198, H.199, F.315, M.331, R.335, S.338, Y.339, T.342, H.343, R.346 Chain D: L.42, D.46 Ligands: O.5 30 PLIP interactions: 28 interactions with chain B, 1 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.54, B:V.55, B:H.56, B:V.127, B:N.129, B:A.139, B:F.142, B:F.142, B:F.142, B:F.142, B:R.335, B:Y.339, B:Y.339, B:T.342, D:L.42 Water bridges: B:V.54, B:A.114, B:A.313, B:R.346 Salt bridges: B:R.53, B:R.53, B:R.93, B:H.343, B:R.346 pi-Stacking: B:H.56, B:F.134, B:F.142 pi-Cation interactions: B:R.335 Metal complexes: B:Y.339, O.5 HEM.7: 28 residues within 4Å: Chain A: L.42, D.46 Chain C: R.53, V.54, V.55, H.56, R.93, G.112, F.113, A.114, V.127, G.128, N.129, F.134, A.139, F.142, G.197, S.198, H.199, F.315, M.331, R.335, S.338, Y.339, T.342, H.343, R.346 Ligands: O.8 32 PLIP interactions: 30 interactions with chain C, 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: C:V.54, C:V.55, C:H.56, C:V.127, C:N.129, C:F.134, C:A.139, C:F.142, C:F.142, C:F.142, C:F.142, C:R.335, C:Y.339, C:Y.339, C:T.342, A:L.42 Water bridges: C:A.114, C:A.313, C:T.342, C:T.342, C:R.346 Salt bridges: C:R.53, C:R.53, C:R.93, C:H.343, C:R.346 pi-Stacking: C:H.56, C:F.134, C:F.142 pi-Cation interactions: C:R.335 Metal complexes: C:Y.339, O.8 HEM.9: 27 residues within 4Å: Chain B: L.42, D.46 Chain D: R.53, V.54, V.55, H.56, R.93, G.112, F.113, A.114, V.127, G.128, N.129, A.139, F.142, G.197, S.198, H.199, F.315, M.331, R.335, S.338, Y.339, T.342, H.343, R.346 Ligands: O.10 30 PLIP interactions: 28 interactions with chain D, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: D:V.54, D:V.55, D:H.56, D:V.127, D:N.129, D:A.139, D:F.142, D:F.142, D:F.142, D:F.142, D:R.335, D:Y.339, D:Y.339, D:T.342, B:L.42 Water bridges: D:V.54, D:A.114, D:A.313, D:R.346 Salt bridges: D:R.53, D:R.53, D:R.93, D:H.343, D:R.346 pi-Stacking: D:H.56, D:F.134, D:F.142 pi-Cation interactions: D:R.335 Metal complexes: D:Y.339, O.10

4 x O: OXYGEN ATOM(Non-covalent)

O.3: 5 residues within 4Å: Chain A: V.55, H.56, F.142, Y.339 Ligands: HEM.2 No protein-ligand interaction detected (PLIP) O.5: 5 residues within 4Å: Chain B: V.55, H.56, F.142, Y.339 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) O.8: 5 residues within 4Å: Chain C: V.55, H.56, F.142, Y.339 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) O.10: 5 residues within 4Å: Chain D: V.55, H.56, F.142, Y.339 Ligands: HEM.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alfonso-Prieto, M. et al., The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations. J.Am.Chem.Soc. (2007)

Release Date

2007-08-28

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Catalase

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