SMTL ID : 1m85.1

Structure of Proteus mirabilis catalase for the native form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

32 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: R.182, H.192, R.216 Ligand excluded by PLIP SO4.2: 2 residues within 4Å: Chain A: S.420, R.423 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: S.430, D.432, R.436 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.182, I.221, N.223 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: P.283, H.284, A.285 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: R.216, Q.218, Q.259 Ligand excluded by PLIP SO4.7: 1 residues within 4Å: Chain D: R.242 Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain A: R.45 Chain B: R.45 Chain C: R.342, Y.343 Chain D: R.342, Y.343 Ligands: SO4.18 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: R.182, H.192, R.216 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain B: S.420, R.423 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: S.430, D.432, R.436 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: R.182, I.221, N.223 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: P.283, H.284, A.285 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain B: R.216, Q.218, Q.259 Ligand excluded by PLIP SO4.17: 1 residues within 4Å: Chain C: R.242 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain A: R.45 Chain B: R.45 Chain C: R.342, Y.343 Chain D: R.342, Y.343 Ligands: SO4.8 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: R.182, H.192, R.216 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain C: S.420, R.423 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: S.430, D.432, R.436 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain C: R.182, I.221, N.223 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain C: P.283, H.284, A.285 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain C: R.216, Q.218, Q.259 Ligand excluded by PLIP SO4.27: 1 residues within 4Å: Chain B: R.242 Ligand excluded by PLIP SO4.28: 7 residues within 4Å: Chain A: R.342, Y.343 Chain B: R.342, Y.343 Chain C: R.45 Chain D: R.45 Ligands: SO4.38 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain D: R.182, H.192, R.216 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain D: S.420, R.423 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain D: S.430, D.432, R.436 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain D: R.182, I.221, N.223 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain D: P.283, H.284, A.285 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain D: R.216, Q.218, Q.259 Ligand excluded by PLIP SO4.37: 1 residues within 4Å: Chain A: R.242 Ligand excluded by PLIP SO4.38: 7 residues within 4Å: Chain A: R.342, Y.343 Chain B: R.342, Y.343 Chain C: R.45 Chain D: R.45 Ligands: SO4.28 Ligand excluded by PLIP

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

HEM.9: 27 residues within 4Å: Chain A: R.51, M.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, F.132, P.137, F.140, G.195, S.196, H.197, L.278, F.313, M.329, R.333, S.336, Y.337, A.340, H.341, R.344 Chain D: L.40, D.44 28 PLIP interactions: 27 interactions with chain A, 1 interactions with chain D, Hydrophobic interactions: A:H.54, A:A.112, A:V.125, A:N.127, A:F.132, A:P.137, A:F.140, A:F.140, A:F.140, A:F.140, A:L.278, A:R.333, A:Y.337, A:Y.337, A:A.340, D:L.40 Water bridges: A:A.112, A:A.311, A:R.344 Salt bridges: A:R.51, A:R.51, A:R.91, A:H.341, A:R.344 pi-Stacking: A:F.132, A:F.140 pi-Cation interactions: A:R.333 Metal complexes: A:Y.337 HEM.19: 27 residues within 4Å: Chain B: R.51, M.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, F.132, P.137, F.140, G.195, S.196, H.197, L.278, F.313, M.329, R.333, S.336, Y.337, A.340, H.341, R.344 Chain C: L.40, D.44 28 PLIP interactions: 27 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:H.54, B:A.112, B:V.125, B:N.127, B:F.132, B:P.137, B:F.140, B:F.140, B:F.140, B:F.140, B:L.278, B:R.333, B:Y.337, B:Y.337, B:A.340, C:L.40 Water bridges: B:A.112, B:A.311, B:R.344 Salt bridges: B:R.51, B:R.51, B:R.91, B:H.341, B:R.344 pi-Stacking: B:F.132, B:F.140 pi-Cation interactions: B:R.333 Metal complexes: B:Y.337 HEM.29: 27 residues within 4Å: Chain B: L.40, D.44 Chain C: R.51, M.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, F.132, P.137, F.140, G.195, S.196, H.197, L.278, F.313, M.329, R.333, S.336, Y.337, A.340, H.341, R.344 28 PLIP interactions: 27 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:H.54, C:A.112, C:V.125, C:N.127, C:F.132, C:P.137, C:F.140, C:F.140, C:F.140, C:F.140, C:L.278, C:R.333, C:Y.337, C:Y.337, C:A.340, B:L.40 Water bridges: C:A.112, C:A.311, C:R.344 Salt bridges: C:R.51, C:R.51, C:R.91, C:H.341, C:R.344 pi-Stacking: C:F.132, C:F.140 pi-Cation interactions: C:R.333 Metal complexes: C:Y.337 HEM.39: 27 residues within 4Å: Chain A: L.40, D.44 Chain D: R.51, M.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, F.132, P.137, F.140, G.195, S.196, H.197, L.278, F.313, M.329, R.333, S.336, Y.337, A.340, H.341, R.344 28 PLIP interactions: 27 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: D:H.54, D:A.112, D:V.125, D:N.127, D:F.132, D:P.137, D:F.140, D:F.140, D:F.140, D:F.140, D:L.278, D:R.333, D:Y.337, D:Y.337, D:A.340, A:L.40 Water bridges: D:A.112, D:A.311, D:R.344 Salt bridges: D:R.51, D:R.51, D:R.91, D:H.341, D:R.344 pi-Stacking: D:F.132, D:F.140 pi-Cation interactions: D:R.333 Metal complexes: D:Y.337

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: G.338, R.342, H.349 Chain C: A.9, E.38, H.42 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:G.338, A:R.342, C:E.38 Water bridges: A:N.317, A:R.342, C:A.9, C:V.34, C:E.38, C:E.38 GOL.20: 6 residues within 4Å: Chain B: G.338, R.342, H.349 Chain D: A.9, E.38, H.42 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:E.38, B:G.338, B:R.342 Water bridges: D:A.9, D:V.34, D:E.38, D:E.38, B:N.317, B:R.342 GOL.30: 6 residues within 4Å: Chain A: A.9, E.38, H.42 Chain C: G.338, R.342, H.349 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Water bridges: A:A.9, A:V.34, A:E.38, A:E.38, C:N.317, C:R.342 Hydrogen bonds: C:G.338, C:R.342 GOL.40: 6 residues within 4Å: Chain B: A.9, E.38, H.42 Chain D: G.338, R.342, H.349 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:G.338, D:R.342 Water bridges: D:N.317, D:R.342, B:A.9, B:V.34, B:E.38, B:E.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gouet, P. et al., Crystal structure of Proteus mirabilis PR catalase with and without bound NADPH. J.Mol.Biol. (1995)

Release Date

2002-08-14

Peptides

catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

catalase

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