SMTL ID : 1qwl.1

Structure of Helicobacter pylori catalase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

2 x AZI: AZIDE ION(Non-covalent)

AZI.1: 5 residues within 4Å: Chain A: R.344, Y.345 Chain B: Y.345 Chain C: R.47 Chain D: R.47 7 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 interactions with chain D, 2 interactions with chain C Water bridges: B:R.344, A:R.344, A:Y.345, C:R.47 Hydrogen bonds: D:R.47, D:R.47, C:R.47 AZI.5: 5 residues within 4Å: Chain A: R.47 Chain B: R.47 Chain C: R.344, Y.345 Chain D: Y.345 7 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:R.47, B:R.47, A:R.47 Water bridges: C:R.344, C:Y.345, A:R.47, D:R.344

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(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: OXY.4 31 PLIP interactions: 30 interactions with chain A, 1 interactions with chain C, 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 HEM.3: 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, 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 D: L.42, D.46 29 PLIP interactions: 28 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:V.54, B:V.55, B:H.56, B:V.127, B:N.129, B:F.134, B:A.139, B:F.142, B:F.142, B:F.142, B:F.142, B:R.335, 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 HEM.6: 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: OXY.8 31 PLIP interactions: 30 interactions with chain C, 1 interactions with chain A, 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 HEM.7: 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, 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 29 PLIP interactions: 28 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:V.54, D:V.55, D:H.56, D:V.127, D:N.129, D:F.134, D:A.139, D:F.142, D:F.142, D:F.142, D:F.142, D:R.335, 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

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 5 residues within 4Å: Chain A: V.55, H.56, F.142, Y.339 Ligands: HEM.2 No protein-ligand interaction detected (PLIP) OXY.8: 5 residues within 4Å: Chain C: V.55, H.56, F.142, Y.339 Ligands: HEM.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loewen, P.C. et al., Structure of Helicobacter pylori Catalase, with and without Formic Acid Bound, at 1.6 A Resolution. Biochemistry (2004)

Release Date

2004-03-30

Peptides

KatA catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

KatA catalase

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