SMTL ID : 1itk.2 (1 other biounit)

Crystal structure of catalase-peroxidase from Haloarcula marismortui

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: Q.239, R.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.239 Water bridges: A:D.242 Salt bridges: A:R.243 SO4.2: 3 residues within 4Å: Chain A: P.282, I.283 Chain B: R.684 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.283 Water bridges: A:E.284, A:E.284, B:R.684 Salt bridges: B:R.684 SO4.3: 5 residues within 4Å: Chain A: K.580, I.592, T.593, R.594, V.599 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.593, A:T.593, A:R.594 Salt bridges: A:K.580, A:R.594 SO4.4: 3 residues within 4Å: Chain A: R.684 Chain B: P.282, I.283 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.283 Water bridges: A:R.684 Salt bridges: A:R.684 SO4.19: 2 residues within 4Å: Chain B: Q.239, R.243 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.239, B:D.242 Water bridges: B:R.243 Salt bridges: B:R.243 SO4.20: 5 residues within 4Å: Chain B: K.580, I.592, T.593, R.594, V.599 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.593, B:R.594 Salt bridges: B:K.580, B:R.594 SO4.31: 2 residues within 4Å: Chain C: Q.239, R.243 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.239 Salt bridges: C:R.243 SO4.32: 3 residues within 4Å: Chain C: P.282, I.283 Chain D: R.684 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.283 Water bridges: C:E.284, C:E.284, D:R.684 Salt bridges: D:R.684 SO4.33: 5 residues within 4Å: Chain C: K.580, I.592, T.593, R.594, V.599 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.593, C:T.593, C:R.594 Salt bridges: C:K.580, C:R.594 SO4.34: 3 residues within 4Å: Chain C: R.684 Chain D: P.282, I.283 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:R.684 Salt bridges: C:R.684 Hydrogen bonds: D:I.283 SO4.49: 2 residues within 4Å: Chain D: Q.239, R.243 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.239 Water bridges: D:R.243 Salt bridges: D:R.243 SO4.50: 5 residues within 4Å: Chain D: K.580, I.592, T.593, R.594, V.599 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.593, D:R.594 Salt bridges: D:K.580, D:R.594

32 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: S.212, V.219, N.220, P.224, N.236 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: A.611, S.612 Chain B: G.44 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: V.581, D.582, G.583, L.600, N.603 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: Y.329, E.330, W.331, K.376, R.377 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain A: T.569, D.570, A.571, P.572 Chain C: P.566, E.567 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: N.186, W.187 Chain B: P.20, K.21 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: V.46, E.47, Q.145 Chain B: K.710 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: P.20, K.21 Chain B: N.186, W.187 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: L.490, E.491, P.566 Chain C: E.491 Ligands: CL.43 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: G.481, R.487, F.574 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: G.108, R.114, I.120, W.187 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: V.213, N.220, D.225 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain A: V.43, G.44 Chain B: A.611, S.612 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain A: K.710 Chain B: V.46, E.47, Q.145 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain B: G.108, R.114, I.120 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: V.581, D.582, G.583, N.603 Ligand excluded by PLIP CL.35: 5 residues within 4Å: Chain C: S.212, V.219, N.220, P.224, N.236 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain C: A.611, S.612 Chain D: G.44 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain C: V.581, D.582, G.583, L.600, N.603 Ligand excluded by PLIP CL.38: 5 residues within 4Å: Chain C: Y.329, E.330, W.331, K.376, R.377 Ligand excluded by PLIP CL.39: 6 residues within 4Å: Chain A: P.566, E.567 Chain C: T.569, D.570, A.571, P.572 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain C: N.186, W.187 Chain D: P.20, K.21 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain C: V.46, E.47, Q.145 Chain D: K.710 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain C: P.20, K.21 Chain D: N.186, W.187 Ligand excluded by PLIP CL.43: 5 residues within 4Å: Chain A: E.491 Chain C: L.490, E.491, P.566 Ligands: CL.13 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain C: G.481, R.487, F.574 Ligand excluded by PLIP CL.45: 4 residues within 4Å: Chain C: G.108, R.114, I.120, W.187 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain C: V.213, N.220, D.225 Ligand excluded by PLIP CL.51: 4 residues within 4Å: Chain C: V.43, G.44 Chain D: A.611, S.612 Ligand excluded by PLIP CL.52: 4 residues within 4Å: Chain C: K.710 Chain D: V.46, E.47, Q.145 Ligand excluded by PLIP CL.53: 3 residues within 4Å: Chain D: G.108, R.114, I.120 Ligand excluded by PLIP CL.54: 4 residues within 4Å: Chain D: V.581, D.582, G.583, N.603 Ligand excluded by PLIP

12 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.17: 3 residues within 4Å: Chain A: K.401, M.427, W.429 No protein-ligand interaction detected (PLIP) UNX.25: 5 residues within 4Å: Chain B: S.212, V.219, N.220, P.224, N.236 No protein-ligand interaction detected (PLIP) UNX.26: 3 residues within 4Å: Chain B: G.481, R.487, F.574 No protein-ligand interaction detected (PLIP) UNX.27: 5 residues within 4Å: Chain B: Y.329, E.330, W.331, K.376, R.377 No protein-ligand interaction detected (PLIP) UNX.28: 3 residues within 4Å: Chain B: V.213, N.220, D.225 No protein-ligand interaction detected (PLIP) UNX.29: 2 residues within 4Å: Chain B: M.427, W.429 No protein-ligand interaction detected (PLIP) UNX.47: 3 residues within 4Å: Chain C: K.401, M.427, W.429 No protein-ligand interaction detected (PLIP) UNX.55: 5 residues within 4Å: Chain D: S.212, V.219, N.220, P.224, N.236 No protein-ligand interaction detected (PLIP) UNX.56: 3 residues within 4Å: Chain D: G.481, R.487, F.574 No protein-ligand interaction detected (PLIP) UNX.57: 5 residues within 4Å: Chain D: Y.329, E.330, W.331, K.376, R.377 No protein-ligand interaction detected (PLIP) UNX.58: 3 residues within 4Å: Chain D: V.213, N.220, D.225 No protein-ligand interaction detected (PLIP) UNX.59: 2 residues within 4Å: Chain D: M.427, W.429 No protein-ligand interaction detected (PLIP)

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

HEM.18: 25 residues within 4Å: Chain A: P.88, L.89, I.91, R.92, W.95, V.219, P.221, I.237, F.241, L.254, I.255, G.258, H.259, F.261, G.262, K.263, V.264, H.265, T.304, S.305, W.311, L.369, T.371, F.399, W.403 28 PLIP interactions: 27 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.91, A:R.92, A:W.95, A:W.95, A:W.95, A:I.237, A:F.241, A:L.254, A:I.255, A:V.264, A:W.311, A:W.311, A:T.371, A:F.399, A:W.403 Hydrogen bonds: A:K.263, A:H.265, A:T.304, A:S.305 Water bridges: A:R.92, A:N.128, A:H.265 Salt bridges: A:R.92, A:H.265, A:H.265 pi-Stacking: A:W.95 Metal complexes: A:H.259, H2O.25 HEM.30: 25 residues within 4Å: Chain B: P.88, L.89, I.91, R.92, W.95, V.219, P.221, I.237, F.241, L.254, I.255, G.258, H.259, F.261, G.262, K.263, V.264, H.265, T.304, S.305, W.311, L.369, T.371, F.399, W.403 30 PLIP interactions: 30 interactions with chain B, Hydrophobic interactions: B:I.91, B:R.92, B:W.95, B:W.95, B:I.237, B:F.241, B:L.254, B:I.255, B:V.264, B:W.311, B:W.311, B:L.369, B:T.371, B:F.399, B:W.403 Hydrogen bonds: B:K.263, B:H.265, B:T.304, B:S.305 Water bridges: B:D.82, B:D.82, B:R.92, B:R.92, B:H.265, B:H.265 Salt bridges: B:R.92, B:H.265, B:H.265 pi-Stacking: B:W.95 Metal complexes: B:H.259 HEM.48: 25 residues within 4Å: Chain C: P.88, L.89, I.91, R.92, W.95, V.219, P.221, I.237, F.241, L.254, I.255, G.258, H.259, F.261, G.262, K.263, V.264, H.265, T.304, S.305, W.311, L.369, T.371, F.399, W.403 29 PLIP interactions: 28 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:I.91, C:R.92, C:W.95, C:W.95, C:W.95, C:I.237, C:F.241, C:L.254, C:I.255, C:V.264, C:W.311, C:W.311, C:T.371, C:F.399, C:W.403 Hydrogen bonds: C:K.263, C:H.265, C:S.305 Water bridges: C:D.82, C:D.82, C:R.92, C:N.128, C:H.265 Salt bridges: C:R.92, C:H.265, C:H.265 pi-Stacking: C:W.95 Metal complexes: C:H.259, H2O.78 HEM.60: 25 residues within 4Å: Chain D: P.88, L.89, I.91, R.92, W.95, V.219, P.221, I.237, F.241, L.254, I.255, G.258, H.259, F.261, G.262, K.263, V.264, H.265, T.304, S.305, W.311, L.369, T.371, F.399, W.403 27 PLIP interactions: 27 interactions with chain D, Hydrophobic interactions: D:I.91, D:R.92, D:W.95, D:W.95, D:I.237, D:F.241, D:L.254, D:I.255, D:V.264, D:W.311, D:W.311, D:L.369, D:T.371, D:F.399, D:W.403 Hydrogen bonds: D:K.263, D:H.265, D:S.305 Water bridges: D:R.92, D:R.92, D:H.265, D:T.304 Salt bridges: D:R.92, D:H.265, D:H.265 pi-Stacking: D:W.95 Metal complexes: D:H.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamada, Y. et al., The 2.0 A crystal structure of catalase-peroxidase from Haloarcula marismortui. Nat.Struct.Biol. (2002)

Release Date

2002-08-28

Peptides

catalase-peroxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

catalase-peroxidase

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