SMTL ID : 4aj9.1

Catalase 3 from Neurospora crassa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 27 residues within 4Å: Chain A: R.62, V.63, V.64, H.65, R.102, G.121, F.122, A.123, V.136, G.137, N.138, F.143, A.148, F.151, I.211, H.212, F.328, L.344, G.347, R.348, S.351, Y.352, T.355, Q.356, R.359 Chain B: L.51, D.55 33 PLIP interactions: 31 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: A:V.63, A:V.64, A:H.65, A:A.123, A:V.136, A:F.143, A:A.148, A:F.151, A:F.151, A:F.151, A:F.151, A:F.328, A:L.344, A:L.344, A:R.348, A:Y.352, A:Y.352, B:L.51 Hydrogen bonds: A:Q.356 Water bridges: A:V.63, A:R.102, A:A.123, A:T.355 Salt bridges: A:R.62, A:R.62, A:R.102, A:R.359 pi-Stacking: A:H.65, A:F.143, A:F.151 pi-Cation interactions: A:R.348 Metal complexes: A:Y.352, H2O.5 HEM.11: 26 residues within 4Å: Chain A: L.51, D.55 Chain B: R.62, V.63, V.64, H.65, R.102, G.121, F.122, V.136, G.137, N.138, F.143, A.148, F.151, I.211, H.212, F.328, L.344, G.347, R.348, S.351, Y.352, T.355, Q.356, R.359 33 PLIP interactions: 32 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:V.63, B:V.64, B:H.65, B:V.136, B:F.143, B:F.143, B:F.143, B:A.148, B:F.151, B:F.151, B:F.151, B:F.151, B:F.328, B:L.344, B:L.344, B:R.348, B:Y.352, B:Y.352, A:L.51 Hydrogen bonds: B:R.102, B:Q.356 Water bridges: B:V.63, B:A.123, B:T.355 Salt bridges: B:R.62, B:R.62, B:R.102, B:R.359 pi-Stacking: B:H.65, B:F.143, B:F.151 pi-Cation interactions: B:R.348 Metal complexes: B:Y.352 HEM.21: 26 residues within 4Å: Chain C: R.62, V.63, V.64, H.65, R.102, G.121, F.122, V.136, G.137, N.138, F.143, A.148, F.151, I.211, H.212, F.328, L.344, G.347, R.348, S.351, Y.352, T.355, Q.356, R.359 Chain D: L.51, D.55 30 PLIP interactions: 29 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:V.63, C:V.64, C:H.65, C:V.136, C:F.143, C:A.148, C:F.151, C:F.151, C:F.151, C:F.151, C:F.328, C:L.344, C:L.344, C:R.348, C:Y.352, C:Y.352, D:L.51 Hydrogen bonds: C:R.102, C:Q.356 Water bridges: C:A.123, C:T.355, C:T.355 Salt bridges: C:R.62, C:R.62, C:R.102, C:R.359 pi-Stacking: C:H.65, C:F.151 pi-Cation interactions: C:R.348 Metal complexes: C:Y.352 HEM.29: 26 residues within 4Å: Chain C: L.51, D.55 Chain D: R.62, V.63, V.64, H.65, R.102, G.121, F.122, V.136, G.137, N.138, F.143, A.148, F.151, I.211, H.212, F.328, L.344, G.347, R.348, S.351, Y.352, T.355, Q.356, R.359 31 PLIP interactions: 30 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:V.63, D:V.64, D:H.65, D:V.136, D:F.143, D:A.148, D:F.151, D:F.151, D:F.151, D:F.151, D:F.328, D:L.344, D:L.344, D:R.348, D:Y.352, D:Y.352, D:T.355, C:L.51 Hydrogen bonds: D:Q.356 Water bridges: D:V.63, D:R.102, D:A.123, D:T.355 Salt bridges: D:R.62, D:R.62, D:R.102, D:R.359 pi-Stacking: D:H.65, D:F.151 pi-Cation interactions: D:R.348 Metal complexes: D:Y.352

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 7 residues within 4Å: Chain A: V.106, A.107, D.118, V.119, F.144, I.155, V.158 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.106, A:F.144, A:I.155, A:V.158 Hydrogen bonds: A:A.107, A:V.119 Water bridges: A:D.118, A:D.118 ACT.3: 8 residues within 4Å: Chain A: N.139, N.197, P.200, H.205, M.206, K.236, A.237, I.521 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.200, A:I.521 Hydrogen bonds: A:N.139, A:N.197 Water bridges: A:N.197, A:D.207, A:K.236 ACT.12: 7 residues within 4Å: Chain B: V.106, A.107, D.118, V.119, F.144, I.155, V.158 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.106, B:F.144, B:I.155, B:V.158 Hydrogen bonds: B:A.107, B:V.119 ACT.13: 8 residues within 4Å: Chain B: N.139, N.197, P.200, H.205, M.206, K.236, A.237, I.521 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.200, B:I.521 Hydrogen bonds: B:N.139, B:D.207 Water bridges: B:N.197, B:N.197, B:N.197 ACT.22: 7 residues within 4Å: Chain C: V.106, A.107, D.118, V.119, F.144, I.155, V.158 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.106, C:F.144, C:I.155, C:V.158 Water bridges: C:D.118, C:V.119 ACT.23: 8 residues within 4Å: Chain C: N.139, N.197, P.200, H.205, M.206, K.236, A.237, I.521 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:P.200, C:I.521 Hydrogen bonds: C:N.139, C:N.197 Water bridges: C:N.197, C:D.207, C:D.207, C:K.236 ACT.30: 7 residues within 4Å: Chain D: V.106, A.107, D.118, V.119, F.144, I.155, V.158 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.106, D:F.144, D:I.155, D:V.158 Hydrogen bonds: D:V.119 ACT.31: 8 residues within 4Å: Chain D: N.139, N.197, P.200, H.205, M.206, K.236, A.237, I.521 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:P.200, D:I.521 Hydrogen bonds: D:N.139 Water bridges: D:N.197, D:N.197, D:N.197, D:D.207, D:D.207

24 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 3 residues within 4Å: Chain A: Y.401, L.402, K.404 Ligand excluded by PLIP 1PE.5: 4 residues within 4Å: Chain A: R.215, E.280, G.423, R.424 Ligand excluded by PLIP 1PE.6: 2 residues within 4Å: Chain A: L.671, E.672 Ligand excluded by PLIP 1PE.7: 4 residues within 4Å: Chain A: E.300, F.301, N.514, V.515 Ligand excluded by PLIP 1PE.8: 7 residues within 4Å: Chain A: Q.615, T.618, R.622 Chain B: S.614, Q.615, T.618 Ligands: 1PE.9 Ligand excluded by PLIP 1PE.9: 5 residues within 4Å: Chain A: F.598, A.603, S.614 Chain B: R.622 Ligands: 1PE.8 Ligand excluded by PLIP 1PE.10: 4 residues within 4Å: Chain A: T.563, D.574, Q.575, A.584 Ligand excluded by PLIP 1PE.14: 4 residues within 4Å: Chain B: R.372, G.376, V.377, W.389 Ligand excluded by PLIP 1PE.15: 4 residues within 4Å: Chain B: S.161, D.163, N.164 Chain D: I.394 Ligand excluded by PLIP 1PE.16: 2 residues within 4Å: Chain B: T.509, Y.510 Ligand excluded by PLIP 1PE.17: 3 residues within 4Å: Chain B: Y.286, G.287, F.301 Ligand excluded by PLIP 1PE.18: 3 residues within 4Å: Chain B: T.563, D.574, Q.575 Ligand excluded by PLIP 1PE.19: 4 residues within 4Å: Chain B: N.450, S.451, L.452, V.515 Ligand excluded by PLIP 1PE.20: 6 residues within 4Å: Chain B: W.81, I.84, L.304, Q.305, V.306, L.307 Ligand excluded by PLIP 1PE.24: 5 residues within 4Å: Chain C: E.300, F.301, L.447, N.514, V.515 Ligand excluded by PLIP 1PE.25: 3 residues within 4Å: Chain C: R.215, E.280, G.423 Ligand excluded by PLIP 1PE.26: 3 residues within 4Å: Chain C: D.440, T.509, Y.510 Ligand excluded by PLIP 1PE.27: 3 residues within 4Å: Chain C: Y.401, L.402, K.404 Ligand excluded by PLIP 1PE.28: 4 residues within 4Å: Chain C: T.563, D.574, Q.575, A.584 Ligand excluded by PLIP 1PE.32: 3 residues within 4Å: Chain A: E.8 Chain D: R.372, W.389 Ligand excluded by PLIP 1PE.33: 4 residues within 4Å: Chain D: Y.621, R.622, I.640, V.642 Ligand excluded by PLIP 1PE.34: 3 residues within 4Å: Chain D: Y.401, L.402, K.404 Ligand excluded by PLIP 1PE.35: 5 residues within 4Å: Chain D: Q.284, G.287, F.288, A.436, T.437 Ligand excluded by PLIP 1PE.36: 8 residues within 4Å: Chain D: P.298, E.300, F.301, T.443, H.512, N.514, V.515, T.516 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zarate-Romero, A. et al., X-ray driven reduction of Cpd I of Catalase-3 from N. crassa reveals differential sensitivity of active sites and formation of ferrous state. Arch.Biochem.Biophys. (2019)

Release Date

2013-03-06

Peptides

CATALASE-3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CATALASE-3