SMTL ID : 6pt7.1

Structure of KatE1 catalase from Acinetobacter sp. Ver3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 17 residues within 4Å: Chain A: P.131, H.174, I.178, S.181, R.183, H.193, H.215, R.217, I.222, V.282, W.283, P.284, K.285, Q.423, A.426, L.427, L.430 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.131, A:V.282 Hydrogen bonds: A:H.174, A:S.181, A:S.181, A:R.217, A:W.283, A:K.285, A:K.285, A:K.285 Water bridges: A:Q.262, A:W.283, A:G.286 Salt bridges: A:R.183, A:H.193, A:R.217, A:K.285 pi-Cation interactions: A:R.183, A:R.183 NAP.7: 17 residues within 4Å: Chain B: P.131, H.174, I.178, S.181, R.183, H.193, H.215, R.217, I.222, V.282, W.283, P.284, K.285, Q.423, A.426, L.427, L.430 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:P.131, B:V.282 Hydrogen bonds: B:H.174, B:S.181, B:S.181, B:R.217, B:W.283, B:K.285, B:K.285, B:K.285 Water bridges: B:Q.262, B:W.283, B:G.286 Salt bridges: B:R.183, B:H.193, B:R.217, B:K.285 pi-Cation interactions: B:R.183, B:R.183 NAP.13: 17 residues within 4Å: Chain C: P.131, H.174, I.178, S.181, R.183, H.193, H.215, R.217, I.222, V.282, W.283, P.284, K.285, Q.423, A.426, L.427, L.430 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:P.131, C:V.282 Hydrogen bonds: C:H.174, C:S.181, C:S.181, C:R.217, C:W.283, C:K.285, C:K.285, C:K.285 Water bridges: C:Q.262, C:W.283, C:G.286 Salt bridges: C:R.183, C:H.193, C:R.217, C:K.285 pi-Cation interactions: C:R.183, C:R.183 NAP.19: 17 residues within 4Å: Chain D: P.131, H.174, I.178, S.181, R.183, H.193, H.215, R.217, I.222, V.282, W.283, P.284, K.285, Q.423, A.426, L.427, L.430 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:P.131, D:V.282 Hydrogen bonds: D:H.174, D:S.181, D:S.181, D:R.217, D:W.283, D:K.285, D:K.285, D:K.285 Water bridges: D:Q.262, D:W.283, D:G.286 Salt bridges: D:R.183, D:H.193, D:R.217, D:K.285 pi-Cation interactions: D:R.183, D:R.183

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

HEM.2: 25 residues within 4Å: Chain A: R.52, M.54, H.55, R.92, G.111, F.112, A.113, V.126, G.127, N.128, A.138, F.141, G.196, S.197, H.198, L.279, F.314, M.330, A.333, R.334, N.337, Y.338, A.341, R.345 Chain D: V.45 27 PLIP interactions: 26 interactions with chain A, 1 interactions with chain D, Hydrophobic interactions: A:H.55, A:V.126, A:N.128, A:A.138, A:F.141, A:F.141, A:F.141, A:F.141, A:L.279, A:F.314, A:A.333, A:R.334, A:Y.338, A:Y.338, A:A.341, D:V.45 Water bridges: A:R.92, A:A.312, A:R.345 Salt bridges: A:R.52, A:R.92, A:R.345 pi-Stacking: A:H.55, A:F.133, A:F.141 pi-Cation interactions: A:R.334 Metal complexes: A:Y.338 HEM.8: 25 residues within 4Å: Chain B: R.52, M.54, H.55, R.92, G.111, F.112, A.113, V.126, G.127, N.128, A.138, F.141, G.196, S.197, H.198, L.279, F.314, M.330, A.333, R.334, N.337, Y.338, A.341, R.345 Chain C: V.45 27 PLIP interactions: 26 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:H.55, B:V.126, B:N.128, B:A.138, B:F.141, B:F.141, B:F.141, B:F.141, B:L.279, B:F.314, B:A.333, B:R.334, B:Y.338, B:Y.338, B:A.341, C:V.45 Water bridges: B:R.92, B:A.312, B:R.345 Salt bridges: B:R.52, B:R.92, B:R.345 pi-Stacking: B:H.55, B:F.133, B:F.141 pi-Cation interactions: B:R.334 Metal complexes: B:Y.338 HEM.14: 25 residues within 4Å: Chain B: V.45 Chain C: R.52, M.54, H.55, R.92, G.111, F.112, A.113, V.126, G.127, N.128, A.138, F.141, G.196, S.197, H.198, L.279, F.314, M.330, A.333, R.334, N.337, Y.338, A.341, R.345 27 PLIP interactions: 26 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:H.55, C:V.126, C:N.128, C:A.138, C:F.141, C:F.141, C:F.141, C:F.141, C:L.279, C:F.314, C:A.333, C:R.334, C:Y.338, C:Y.338, C:A.341, B:V.45 Water bridges: C:R.92, C:A.312, C:R.345 Salt bridges: C:R.52, C:R.92, C:R.345 pi-Stacking: C:H.55, C:F.133, C:F.141 pi-Cation interactions: C:R.334 Metal complexes: C:Y.338 HEM.20: 25 residues within 4Å: Chain A: V.45 Chain D: R.52, M.54, H.55, R.92, G.111, F.112, A.113, V.126, G.127, N.128, A.138, F.141, G.196, S.197, H.198, L.279, F.314, M.330, A.333, R.334, N.337, Y.338, A.341, R.345 27 PLIP interactions: 26 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: D:H.55, D:V.126, D:N.128, D:A.138, D:F.141, D:F.141, D:F.141, D:F.141, D:L.279, D:F.314, D:A.333, D:R.334, D:Y.338, D:Y.338, D:A.341, A:V.45 Water bridges: D:R.92, D:A.312, D:R.345 Salt bridges: D:R.52, D:R.92, D:R.345 pi-Stacking: D:H.55, D:F.133, D:F.141 pi-Cation interactions: D:R.334 Metal complexes: D:Y.338

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

CL.3: 4 residues within 4Å: Chain A: R.46 Chain C: R.46 Chain D: Y.344 Ligands: CL.15 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: R.46 Chain C: Y.344 Chain D: R.46 Ligands: CL.21 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: R.46 Chain B: Y.344 Chain C: R.46 Ligands: CL.3 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain A: Y.344 Chain B: R.46 Chain D: R.46 Ligands: CL.9 Ligand excluded by PLIP

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

UNX.4: 1 residues within 4Å: Ligands: UNX.22 No protein-ligand interaction detected (PLIP) UNX.5: 6 residues within 4Å: Chain A: F.336 Chain C: F.336 Chain D: N.38 Ligands: UNX.6, UNX.17, UNX.18 No protein-ligand interaction detected (PLIP) UNX.6: 6 residues within 4Å: Chain C: F.336 Chain D: A.32, N.38 Ligands: UNX.5, UNX.17, UNX.18 No protein-ligand interaction detected (PLIP) UNX.10: 1 residues within 4Å: Ligands: UNX.16 No protein-ligand interaction detected (PLIP) UNX.11: 6 residues within 4Å: Chain B: F.336 Chain C: N.38 Chain D: F.336 Ligands: UNX.12, UNX.23, UNX.24 No protein-ligand interaction detected (PLIP) UNX.12: 6 residues within 4Å: Chain C: A.32, N.38 Chain D: F.336 Ligands: UNX.11, UNX.23, UNX.24 No protein-ligand interaction detected (PLIP) UNX.16: 1 residues within 4Å: Ligands: UNX.10 No protein-ligand interaction detected (PLIP) UNX.17: 6 residues within 4Å: Chain A: F.336 Chain B: N.38 Chain C: F.336 Ligands: UNX.5, UNX.6, UNX.18 No protein-ligand interaction detected (PLIP) UNX.18: 6 residues within 4Å: Chain A: F.336 Chain B: A.32, N.38 Ligands: UNX.5, UNX.6, UNX.17 No protein-ligand interaction detected (PLIP) UNX.22: 1 residues within 4Å: Ligands: UNX.4 No protein-ligand interaction detected (PLIP) UNX.23: 6 residues within 4Å: Chain A: N.38 Chain B: F.336 Chain D: F.336 Ligands: UNX.11, UNX.12, UNX.24 No protein-ligand interaction detected (PLIP) UNX.24: 6 residues within 4Å: Chain A: A.32, N.38 Chain B: F.336 Ligands: UNX.11, UNX.12, UNX.23 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sartorio, M.G. et al., Structure and functional properties of the cold-adapted catalase from Acinetobacter sp. Ver3 native to the Atacama plateau in northern Argentina. Acta Crystallogr.,Sect.D (2021)

Release Date

2020-07-22

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Catalase