- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-tetramer
- Ligands
- 2 x AZI: AZIDE ION(Non-covalent)
- 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.4
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.3: 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.5
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.43
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.42: 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.44
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.4: 6 residues within 4Å:- Chain A: V.55, H.56, N.129, F.134, F.142
- Ligands: HEM.2
Ligand excluded by PLIPFMT.5: 5 residues within 4Å:- Chain B: H.56, V.97, N.129, F.134
- Ligands: HEM.3
Ligand excluded by PLIPFMT.6: 7 residues within 4Å:- Chain B: R.108, D.109, P.110, F.135, Q.149, W.167, V.180
Ligand excluded by PLIPFMT.7: 4 residues within 4Å:- Chain A: Q.149, V.163, W.167, M.181
Ligand excluded by PLIPFMT.8: 5 residues within 4Å:- Chain B: Q.149, P.158, N.159, V.163
- Ligands: FMT.10
Ligand excluded by PLIPFMT.9: 2 residues within 4Å:- Chain A: P.158, H.160
Ligand excluded by PLIPFMT.10: 3 residues within 4Å:- Chain B: P.158, H.160
- Ligands: FMT.8
Ligand excluded by PLIPFMT.11: 4 residues within 4Å:- Chain B: H.160, E.450, S.451, H.454
Ligand excluded by PLIPFMT.12: 5 residues within 4Å:- Chain A: S.182, D.183, R.184, V.223, E.440
Ligand excluded by PLIPFMT.13: 6 residues within 4Å:- Chain A: K.58, R.101, G.102
- Chain C: R.151, N.156
- Ligands: FMT.37
Ligand excluded by PLIPFMT.14: 2 residues within 4Å:- Chain C: K.150, R.151
Ligand excluded by PLIPFMT.15: 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.23
Ligand excluded by PLIPFMT.16: 4 residues within 4Å:- Chain A: Y.345
- Chain B: R.344
- Chain C: R.47
- Ligands: AZI.1
Ligand excluded by PLIPFMT.17: 5 residues within 4Å:- Chain A: N.130, W.179, R.184, M.193, D.194
Ligand excluded by PLIPFMT.18: 4 residues within 4Å:- Chain A: Y.371
- Chain D: Y.371
- Ligands: FMT.33, FMT.72
Ligand excluded by PLIPFMT.19: 5 residues within 4Å:- Chain A: P.352, Q.353, P.359, F.363
- Chain D: A.11
Ligand excluded by PLIPFMT.20: 3 residues within 4Å:- Chain B: I.283, Y.285, T.286
Ligand excluded by PLIPFMT.21: 3 residues within 4Å:- Chain A: F.247, A.251, N.302
Ligand excluded by PLIPFMT.22: 7 residues within 4Å:- Chain A: K.77, I.204, P.322, G.323, S.396, A.397, R.398
Ligand excluded by PLIPFMT.23: 5 residues within 4Å:- Chain B: K.58, R.101
- Chain D: R.151, N.156
- Ligands: FMT.15
Ligand excluded by PLIPFMT.24: 3 residues within 4Å:- Chain B: R.49, R.101
- Chain D: N.156
Ligand excluded by PLIPFMT.25: 4 residues within 4Å:- Chain A: D.194, H.218, T.219, V.223
Ligand excluded by PLIPFMT.26: 2 residues within 4Å:- Chain A: V.223, K.224
Ligand excluded by PLIPFMT.27: 1 residues within 4Å:- Chain A: K.188
Ligand excluded by PLIPFMT.28: 2 residues within 4Å:- Chain A: K.188, L.226
Ligand excluded by PLIPFMT.29: 3 residues within 4Å:- Chain B: V.223, K.224
- Ligands: FMT.30
Ligand excluded by PLIPFMT.30: 5 residues within 4Å:- Chain B: D.183, H.225, E.440
- Ligands: FMT.29, FMT.32
Ligand excluded by PLIPFMT.31: 2 residues within 4Å:- Chain B: K.188, K.224
Ligand excluded by PLIPFMT.32: 7 residues within 4Å:- Chain B: S.182, D.183, R.184, Y.432, L.436, E.440
- Ligands: FMT.30
Ligand excluded by PLIPFMT.33: 8 residues within 4Å:- Chain A: Y.371
- Chain C: Y.371
- Chain D: P.51, Y.345
- Ligands: FMT.18, FMT.57, FMT.72, FMT.77
Ligand excluded by PLIPFMT.34: 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 PLIPFMT.35: 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.36
Ligand excluded by PLIPFMT.36: 6 residues within 4Å:- Chain A: A.318, R.344
- Chain D: T.36, L.39, E.40
- Ligands: FMT.35
Ligand excluded by PLIPFMT.37: 8 residues within 4Å:- Chain A: A.57, K.58, G.59, R.101, Y.306, E.311
- Chain C: N.156
- Ligands: FMT.13
Ligand excluded by PLIPFMT.38: 5 residues within 4Å:- Chain A: R.344
- Chain B: Y.345
- Chain D: R.47
- Ligands: AZI.1, FMT.72
Ligand excluded by PLIPFMT.39: 7 residues within 4Å:- Chain B: A.318, L.336, R.344
- Chain C: T.36, L.39, E.40
- Ligands: FMT.34
Ligand excluded by PLIPFMT.43: 6 residues within 4Å:- Chain C: V.55, H.56, N.129, F.134, F.142
- Ligands: HEM.41
Ligand excluded by PLIPFMT.44: 5 residues within 4Å:- Chain D: H.56, V.97, N.129, F.134
- Ligands: HEM.42
Ligand excluded by PLIPFMT.45: 7 residues within 4Å:- Chain D: R.108, D.109, P.110, F.135, Q.149, W.167, V.180
Ligand excluded by PLIPFMT.46: 4 residues within 4Å:- Chain C: Q.149, V.163, W.167, M.181
Ligand excluded by PLIPFMT.47: 5 residues within 4Å:- Chain D: Q.149, P.158, N.159, V.163
- Ligands: FMT.49
Ligand excluded by PLIPFMT.48: 2 residues within 4Å:- Chain C: P.158, H.160
Ligand excluded by PLIPFMT.49: 3 residues within 4Å:- Chain D: P.158, H.160
- Ligands: FMT.47
Ligand excluded by PLIPFMT.50: 4 residues within 4Å:- Chain D: H.160, E.450, S.451, H.454
Ligand excluded by PLIPFMT.51: 5 residues within 4Å:- Chain C: S.182, D.183, R.184, V.223, E.440
Ligand excluded by PLIPFMT.52: 6 residues within 4Å:- Chain A: R.151, N.156
- Chain C: K.58, R.101, G.102
- Ligands: FMT.76
Ligand excluded by PLIPFMT.53: 2 residues within 4Å:- Chain A: K.150, R.151
Ligand excluded by PLIPFMT.54: 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.62
Ligand excluded by PLIPFMT.55: 4 residues within 4Å:- Chain A: R.47
- Chain C: Y.345
- Chain D: R.344
- Ligands: AZI.40
Ligand excluded by PLIPFMT.56: 5 residues within 4Å:- Chain C: N.130, W.179, R.184, M.193, D.194
Ligand excluded by PLIPFMT.57: 4 residues within 4Å:- Chain B: Y.371
- Chain C: Y.371
- Ligands: FMT.33, FMT.72
Ligand excluded by PLIPFMT.58: 5 residues within 4Å:- Chain B: A.11
- Chain C: P.352, Q.353, P.359, F.363
Ligand excluded by PLIPFMT.59: 3 residues within 4Å:- Chain D: I.283, Y.285, T.286
Ligand excluded by PLIPFMT.60: 3 residues within 4Å:- Chain C: F.247, A.251, N.302
Ligand excluded by PLIPFMT.61: 7 residues within 4Å:- Chain C: K.77, I.204, P.322, G.323, S.396, A.397, R.398
Ligand excluded by PLIPFMT.62: 5 residues within 4Å:- Chain B: R.151, N.156
- Chain D: K.58, R.101
- Ligands: FMT.54
Ligand excluded by PLIPFMT.63: 3 residues within 4Å:- Chain B: N.156
- Chain D: R.49, R.101
Ligand excluded by PLIPFMT.64: 4 residues within 4Å:- Chain C: D.194, H.218, T.219, V.223
Ligand excluded by PLIPFMT.65: 2 residues within 4Å:- Chain C: V.223, K.224
Ligand excluded by PLIPFMT.66: 1 residues within 4Å:- Chain C: K.188
Ligand excluded by PLIPFMT.67: 2 residues within 4Å:- Chain C: K.188, L.226
Ligand excluded by PLIPFMT.68: 3 residues within 4Å:- Chain D: V.223, K.224
- Ligands: FMT.69
Ligand excluded by PLIPFMT.69: 5 residues within 4Å:- Chain D: D.183, H.225, E.440
- Ligands: FMT.68, FMT.71
Ligand excluded by PLIPFMT.70: 2 residues within 4Å:- Chain D: K.188, K.224
Ligand excluded by PLIPFMT.71: 7 residues within 4Å:- Chain D: S.182, D.183, R.184, Y.432, L.436, E.440
- Ligands: FMT.69
Ligand excluded by PLIPFMT.72: 8 residues within 4Å:- Chain A: Y.371
- Chain B: P.51, Y.345
- Chain C: Y.371
- Ligands: FMT.18, FMT.33, FMT.38, FMT.57
Ligand excluded by PLIPFMT.73: 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 PLIPFMT.74: 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.75
Ligand excluded by PLIPFMT.75: 6 residues within 4Å:- Chain B: T.36, L.39, E.40
- Chain C: A.318, R.344
- Ligands: FMT.74
Ligand excluded by PLIPFMT.76: 8 residues within 4Å:- Chain A: N.156
- Chain C: A.57, K.58, G.59, R.101, Y.306, E.311
- Ligands: FMT.52
Ligand excluded by PLIPFMT.77: 5 residues within 4Å:- Chain B: R.47
- Chain C: R.344
- Chain D: Y.345
- Ligands: FMT.33, AZI.40
Ligand excluded by PLIPFMT.78: 7 residues within 4Å:- Chain A: T.36, L.39, E.40
- Chain D: A.318, L.336, R.344
- Ligands: FMT.73
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
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-tetramer
- Ligands
- 2 x AZI: AZIDE ION(Non-covalent)
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)
- 72 x FMT: FORMIC ACID(Non-functional Binders)
- 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
AB
BC
AD
B