SMTL ID : 1mqf.1

Compound I from Proteus mirabilis catalase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.182, H.192, R.216, I.221 Ligand excluded by PLIP SO4.2: 2 residues within 4Å: Chain A: F.419, 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: 4 residues within 4Å: Chain A: R.216, Q.218, K.257, Q.259 Ligand excluded by PLIP SO4.7: 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: SO4.17 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: R.182, H.192, R.216, I.221 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain B: F.419, 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: 4 residues within 4Å: Chain B: R.216, Q.218, K.257, Q.259 Ligand excluded by PLIP SO4.17: 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: SO4.7 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain C: R.182, H.192, R.216, I.221 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain C: F.419, 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: 4 residues within 4Å: Chain C: R.216, Q.218, K.257, Q.259 Ligand excluded by PLIP SO4.27: 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: SO4.37 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: R.182, H.192, R.216, I.221 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain D: F.419, 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: 4 residues within 4Å: Chain D: R.216, Q.218, K.257, Q.259 Ligand excluded by PLIP SO4.37: 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: SO4.27 Ligand excluded by PLIP

4 x O: OXYGEN ATOM(Non-covalent)

O.8: 5 residues within 4Å: Chain A: M.53, H.54, F.140, Y.337 Ligands: HEM.9 No protein-ligand interaction detected (PLIP) O.18: 5 residues within 4Å: Chain B: M.53, H.54, F.140, Y.337 Ligands: HEM.19 No protein-ligand interaction detected (PLIP) O.28: 5 residues within 4Å: Chain C: M.53, H.54, F.140, Y.337 Ligands: HEM.29 No protein-ligand interaction detected (PLIP) O.38: 5 residues within 4Å: Chain D: M.53, H.54, F.140, Y.337 Ligands: HEM.39 No protein-ligand interaction detected (PLIP)

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

HEM.9: 28 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 Ligands: O.8 27 PLIP interactions: 25 interactions with chain A, 1 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: A:H.54, 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.91, A:H.341, A:R.344 pi-Stacking: A:H.54, A:F.132 pi-Cation interactions: A:R.333 Metal complexes: A:Y.337, O.8 HEM.19: 28 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 Ligands: O.18 27 PLIP interactions: 25 interactions with chain B, 1 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.54, 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.91, B:H.341, B:R.344 pi-Stacking: B:H.54, B:F.132 pi-Cation interactions: B:R.333 Metal complexes: B:Y.337, O.18 HEM.29: 28 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 Ligands: O.28 27 PLIP interactions: 25 interactions with chain C, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: C:H.54, 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.91, C:H.341, C:R.344 pi-Stacking: C:H.54, C:F.132 pi-Cation interactions: C:R.333 Metal complexes: C:Y.337, O.28 HEM.39: 28 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 Ligands: O.38 27 PLIP interactions: 25 interactions with chain D, 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: D:H.54, 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.91, D:H.341, D:R.344 pi-Stacking: D:H.54, D:F.132 pi-Cation interactions: D:R.333 Metal complexes: D:Y.337, O.38

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: R.342, H.349 Chain C: A.9, E.38, H.42 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:G.338, A:R.342, C:E.38 Water bridges: C:E.38, C:E.38 GOL.20: 5 residues within 4Å: Chain B: R.342, H.349 Chain D: A.9, E.38, H.42 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:G.338, B:R.342, D:E.38 Water bridges: D:E.38, D:E.38 GOL.30: 5 residues within 4Å: Chain A: A.9, E.38, H.42 Chain C: R.342, H.349 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Water bridges: A:E.38, A:E.38 Hydrogen bonds: C:G.338, C:R.342 GOL.40: 5 residues within 4Å: Chain B: A.9, E.38, H.42 Chain D: R.342, H.349 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:G.338, D:R.342 Water bridges: B:E.38, B:E.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andreoletti, P. et al., Structural studies of Proteus mirabilis catalase in its ground state, oxidized state and in complex with formic acid. Acta Crystallogr.,Sect.D (2003)

Release Date

2002-10-02

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Catalase

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