SMTL ID : 1qwm.1

Structure of Helicobacter pylori catalase with formic acid bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

2 x AZI: AZIDE ION(Non-covalent)

AZI.1: 7 residues within 4Å: Chain A: R.344, Y.345 Chain B: Y.345 Chain C: R.47 Chain D: R.47 Ligands: FMT.9, FMT.23 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:R.47, D:R.47, C:R.47, A:R.344 AZI.40: 7 residues within 4Å: Chain A: R.47 Chain B: R.47 Chain C: R.344, Y.345 Chain D: Y.345 Ligands: FMT.48, FMT.62 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.47, B:R.47, A:R.47

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

HEM.2: 27 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, 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: FMT.3 30 PLIP interactions: 29 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:V.54, A:V.55, A:H.56, A:A.114, A:V.127, A:N.129, 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:V.54, A:A.114, 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.24: 28 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 Ligands: FMT.25 31 PLIP interactions: 30 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:V.54, B:V.55, B:H.56, B:A.114, 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: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.41: 27 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, 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: FMT.42 30 PLIP interactions: 29 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:V.54, C:V.55, C:H.56, C:A.114, C:V.127, C:N.129, 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:V.54, C:A.114, 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.63: 28 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 Ligands: FMT.64 31 PLIP interactions: 30 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:V.54, D:V.55, D:H.56, D:A.114, 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: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

72 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: V.55, H.56, N.129, F.134, F.142 Ligands: HEM.2 Ligand excluded by PLIP FMT.4: 4 residues within 4Å: Chain A: Q.149, V.163, W.167, M.181 Ligand excluded by PLIP FMT.5: 2 residues within 4Å: Chain A: P.158, H.160 Ligand excluded by PLIP FMT.6: 5 residues within 4Å: Chain A: S.182, D.183, R.184, V.223, E.440 Ligand excluded by PLIP FMT.7: 6 residues within 4Å: Chain A: K.58, R.101, G.102 Chain C: R.151, N.156 Ligands: FMT.22 Ligand excluded by PLIP FMT.8: 2 residues within 4Å: Chain C: K.150, R.151 Ligand excluded by PLIP FMT.9: 4 residues within 4Å: Chain A: Y.345 Chain B: R.344 Chain C: R.47 Ligands: AZI.1 Ligand excluded by PLIP FMT.10: 5 residues within 4Å: Chain A: N.130, W.179, R.184, M.193, D.194 Ligand excluded by PLIP FMT.11: 4 residues within 4Å: Chain A: Y.371 Chain D: Y.371 Ligands: FMT.19, FMT.58 Ligand excluded by PLIP FMT.12: 5 residues within 4Å: Chain A: P.352, Q.353, P.359, F.363 Chain D: A.11 Ligand excluded by PLIP FMT.13: 3 residues within 4Å: Chain A: F.247, A.251, N.302 Ligand excluded by PLIP FMT.14: 7 residues within 4Å: Chain A: K.77, I.204, P.322, G.323, S.396, A.397, R.398 Ligand excluded by PLIP FMT.15: 4 residues within 4Å: Chain A: D.194, H.218, T.219, V.223 Ligand excluded by PLIP FMT.16: 2 residues within 4Å: Chain A: V.223, K.224 Ligand excluded by PLIP FMT.17: 1 residues within 4Å: Chain A: K.188 Ligand excluded by PLIP FMT.18: 2 residues within 4Å: Chain A: K.188, L.226 Ligand excluded by PLIP FMT.19: 8 residues within 4Å: Chain A: Y.371 Chain C: Y.371 Chain D: P.51, Y.345 Ligands: FMT.11, FMT.50, FMT.58, FMT.62 Ligand excluded by PLIP FMT.20: 8 residues within 4Å: Chain A: L.336, F.337, G.340, D.341, R.344 Chain B: F.337 Chain D: L.39 Ligands: FMT.21 Ligand excluded by PLIP FMT.21: 6 residues within 4Å: Chain A: A.318, R.344 Chain D: T.36, L.39, E.40 Ligands: FMT.20 Ligand excluded by PLIP FMT.22: 8 residues within 4Å: Chain A: A.57, K.58, G.59, R.101, Y.306, E.311 Chain C: N.156 Ligands: FMT.7 Ligand excluded by PLIP FMT.23: 5 residues within 4Å: Chain A: R.344 Chain B: Y.345 Chain D: R.47 Ligands: AZI.1, FMT.58 Ligand excluded by PLIP FMT.25: 5 residues within 4Å: Chain B: H.56, V.97, N.129, F.134 Ligands: HEM.24 Ligand excluded by PLIP FMT.26: 7 residues within 4Å: Chain B: R.108, D.109, P.110, F.135, Q.149, W.167, V.180 Ligand excluded by PLIP FMT.27: 5 residues within 4Å: Chain B: Q.149, P.158, N.159, V.163 Ligands: FMT.28 Ligand excluded by PLIP FMT.28: 3 residues within 4Å: Chain B: P.158, H.160 Ligands: FMT.27 Ligand excluded by PLIP FMT.29: 4 residues within 4Å: Chain B: H.160, E.450, S.451, H.454 Ligand excluded by PLIP FMT.30: 9 residues within 4Å: Chain B: A.57, K.58, G.59, R.93, R.101, Y.306, E.311 Chain D: N.156 Ligands: FMT.32 Ligand excluded by PLIP FMT.31: 3 residues within 4Å: Chain B: I.283, Y.285, T.286 Ligand excluded by PLIP FMT.32: 5 residues within 4Å: Chain B: K.58, R.101 Chain D: R.151, N.156 Ligands: FMT.30 Ligand excluded by PLIP FMT.33: 3 residues within 4Å: Chain B: R.49, R.101 Chain D: N.156 Ligand excluded by PLIP FMT.34: 3 residues within 4Å: Chain B: V.223, K.224 Ligands: FMT.35 Ligand excluded by PLIP FMT.35: 5 residues within 4Å: Chain B: D.183, H.225, E.440 Ligands: FMT.34, FMT.37 Ligand excluded by PLIP FMT.36: 2 residues within 4Å: Chain B: K.188, K.224 Ligand excluded by PLIP FMT.37: 7 residues within 4Å: Chain B: S.182, D.183, R.184, Y.432, L.436, E.440 Ligands: FMT.35 Ligand excluded by PLIP FMT.38: 7 residues within 4Å: Chain B: L.336, F.337, G.340, D.341, R.344 Chain C: L.39 Ligands: FMT.39 Ligand excluded by PLIP FMT.39: 7 residues within 4Å: Chain B: A.318, L.336, R.344 Chain C: T.36, L.39, E.40 Ligands: FMT.38 Ligand excluded by PLIP FMT.42: 6 residues within 4Å: Chain C: V.55, H.56, N.129, F.134, F.142 Ligands: HEM.41 Ligand excluded by PLIP FMT.43: 4 residues within 4Å: Chain C: Q.149, V.163, W.167, M.181 Ligand excluded by PLIP FMT.44: 2 residues within 4Å: Chain C: P.158, H.160 Ligand excluded by PLIP FMT.45: 5 residues within 4Å: Chain C: S.182, D.183, R.184, V.223, E.440 Ligand excluded by PLIP FMT.46: 6 residues within 4Å: Chain A: R.151, N.156 Chain C: K.58, R.101, G.102 Ligands: FMT.61 Ligand excluded by PLIP FMT.47: 2 residues within 4Å: Chain A: K.150, R.151 Ligand excluded by PLIP FMT.48: 4 residues within 4Å: Chain A: R.47 Chain C: Y.345 Chain D: R.344 Ligands: AZI.40 Ligand excluded by PLIP FMT.49: 5 residues within 4Å: Chain C: N.130, W.179, R.184, M.193, D.194 Ligand excluded by PLIP FMT.50: 4 residues within 4Å: Chain B: Y.371 Chain C: Y.371 Ligands: FMT.19, FMT.58 Ligand excluded by PLIP FMT.51: 5 residues within 4Å: Chain B: A.11 Chain C: P.352, Q.353, P.359, F.363 Ligand excluded by PLIP FMT.52: 3 residues within 4Å: Chain C: F.247, A.251, N.302 Ligand excluded by PLIP FMT.53: 7 residues within 4Å: Chain C: K.77, I.204, P.322, G.323, S.396, A.397, R.398 Ligand excluded by PLIP FMT.54: 4 residues within 4Å: Chain C: D.194, H.218, T.219, V.223 Ligand excluded by PLIP FMT.55: 2 residues within 4Å: Chain C: V.223, K.224 Ligand excluded by PLIP FMT.56: 1 residues within 4Å: Chain C: K.188 Ligand excluded by PLIP FMT.57: 2 residues within 4Å: Chain C: K.188, L.226 Ligand excluded by PLIP FMT.58: 8 residues within 4Å: Chain A: Y.371 Chain B: P.51, Y.345 Chain C: Y.371 Ligands: FMT.11, FMT.19, FMT.23, FMT.50 Ligand excluded by PLIP FMT.59: 8 residues within 4Å: Chain B: L.39 Chain C: L.336, F.337, G.340, D.341, R.344 Chain D: F.337 Ligands: FMT.60 Ligand excluded by PLIP FMT.60: 6 residues within 4Å: Chain B: T.36, L.39, E.40 Chain C: A.318, R.344 Ligands: FMT.59 Ligand excluded by PLIP FMT.61: 8 residues within 4Å: Chain A: N.156 Chain C: A.57, K.58, G.59, R.101, Y.306, E.311 Ligands: FMT.46 Ligand excluded by PLIP FMT.62: 5 residues within 4Å: Chain B: R.47 Chain C: R.344 Chain D: Y.345 Ligands: FMT.19, AZI.40 Ligand excluded by PLIP FMT.64: 5 residues within 4Å: Chain D: H.56, V.97, N.129, F.134 Ligands: HEM.63 Ligand excluded by PLIP FMT.65: 7 residues within 4Å: Chain D: R.108, D.109, P.110, F.135, Q.149, W.167, V.180 Ligand excluded by PLIP FMT.66: 5 residues within 4Å: Chain D: Q.149, P.158, N.159, V.163 Ligands: FMT.67 Ligand excluded by PLIP FMT.67: 3 residues within 4Å: Chain D: P.158, H.160 Ligands: FMT.66 Ligand excluded by PLIP FMT.68: 4 residues within 4Å: Chain D: H.160, E.450, S.451, H.454 Ligand excluded by PLIP FMT.69: 9 residues within 4Å: Chain B: N.156 Chain D: A.57, K.58, G.59, R.93, R.101, Y.306, E.311 Ligands: FMT.71 Ligand excluded by PLIP FMT.70: 3 residues within 4Å: Chain D: I.283, Y.285, T.286 Ligand excluded by PLIP FMT.71: 5 residues within 4Å: Chain B: R.151, N.156 Chain D: K.58, R.101 Ligands: FMT.69 Ligand excluded by PLIP FMT.72: 3 residues within 4Å: Chain B: N.156 Chain D: R.49, R.101 Ligand excluded by PLIP FMT.73: 3 residues within 4Å: Chain D: V.223, K.224 Ligands: FMT.74 Ligand excluded by PLIP FMT.74: 5 residues within 4Å: Chain D: D.183, H.225, E.440 Ligands: FMT.73, FMT.76 Ligand excluded by PLIP FMT.75: 2 residues within 4Å: Chain D: K.188, K.224 Ligand excluded by PLIP FMT.76: 7 residues within 4Å: Chain D: S.182, D.183, R.184, Y.432, L.436, E.440 Ligands: FMT.74 Ligand excluded by PLIP FMT.77: 7 residues within 4Å: Chain A: L.39 Chain D: L.336, F.337, G.340, D.341, R.344 Ligands: FMT.78 Ligand excluded by PLIP FMT.78: 7 residues within 4Å: Chain A: T.36, L.39, E.40 Chain D: A.318, L.336, R.344 Ligands: FMT.77 Ligand excluded by 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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