SMTL ID : 6nsw.1

X-ray reduced Catalase 3 From N.Crassa in Cpd I state (0.135 MGy)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: R.99, V.100, V.101, H.102, R.139, G.158, F.159, A.160, V.173, G.174, N.175, F.180, A.185, F.188, I.248, H.249, F.365, L.381, R.385, S.388, Y.389, T.392, Q.393, R.396 Chain D: L.88 Ligands: O.8 34 PLIP interactions: 32 interactions with chain A, 1 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: A:V.100, A:V.101, A:H.102, A:A.160, A:V.173, A:F.180, A:F.180, A:A.185, A:F.188, A:F.188, A:F.188, A:F.188, A:F.188, A:F.365, A:L.381, A:L.381, A:R.385, A:Y.389, D:L.88 Hydrogen bonds: A:R.139, A:Q.393 Water bridges: A:A.160, A:T.392, A:R.396, A:R.396 Salt bridges: A:R.99, A:R.99, A:R.139, A:R.396 pi-Stacking: A:H.102, A:F.188 pi-Cation interactions: A:R.385 Metal complexes: A:Y.389, O.8 HEM.10: 28 residues within 4Å: Chain B: R.99, V.100, V.101, H.102, R.139, G.158, F.159, A.160, V.173, G.174, N.175, F.180, A.185, F.188, I.248, H.249, F.365, L.381, G.384, R.385, S.388, Y.389, T.392, Q.393, R.396 Chain C: L.88, D.92 Ligands: O.17 31 PLIP interactions: 1 interactions with chain C, 30 interactions with chain B, Hydrophobic interactions: C:L.88, B:V.100, B:V.101, B:H.102, B:A.160, B:V.173, B:F.180, B:F.180, B:F.180, B:A.185, B:F.188, B:F.188, B:F.188, B:I.248, B:F.365, B:L.381, B:L.381, B:R.385, B:Y.389 Hydrogen bonds: B:Q.393 Water bridges: B:V.100, B:R.139, B:F.365 Salt bridges: B:R.99, B:R.99, B:R.139, B:R.396 pi-Stacking: B:H.102, B:F.188 pi-Cation interactions: B:R.385 Metal complexes: B:Y.389 HEM.20: 26 residues within 4Å: Chain B: L.88, D.92 Chain C: R.99, V.100, V.101, H.102, R.139, G.158, F.159, V.173, G.174, N.175, F.180, A.185, F.188, I.248, H.249, F.365, L.381, R.385, S.388, Y.389, T.392, Q.393, R.396 Ligands: O.30 34 PLIP interactions: 32 interactions with chain C, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: C:V.100, C:V.101, C:H.102, C:V.173, C:F.180, C:F.180, C:A.185, C:F.188, C:F.188, C:F.188, C:F.188, C:F.188, C:F.365, C:L.381, C:L.381, C:R.385, C:Y.389, C:Y.389, B:L.88 Hydrogen bonds: C:Q.393 Water bridges: C:R.139, C:R.139, C:T.392, C:T.392 Salt bridges: C:R.99, C:R.99, C:R.139, C:R.396 pi-Stacking: C:H.102, C:F.180, C:F.188 pi-Cation interactions: C:R.385 Metal complexes: C:Y.389, O.30 HEM.31: 26 residues within 4Å: Chain A: L.88 Chain D: R.99, V.100, V.101, H.102, R.139, G.158, F.159, A.160, V.173, G.174, N.175, F.180, A.185, F.188, I.248, H.249, F.365, L.381, R.385, S.388, Y.389, T.392, Q.393, R.396 Ligands: O.38 33 PLIP interactions: 31 interactions with chain D, 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: D:V.100, D:H.102, D:V.173, D:F.180, D:F.180, D:F.180, D:A.185, D:F.188, D:F.188, D:F.188, D:F.188, D:F.188, D:F.365, D:L.381, D:L.381, D:R.385, D:Y.389, D:Y.389, A:L.88 Hydrogen bonds: D:R.139, D:Q.393 Water bridges: D:V.100, D:A.160, D:T.392 Salt bridges: D:R.99, D:R.99, D:R.139, D:R.396 pi-Stacking: D:H.102, D:F.188 pi-Cation interactions: D:R.385 Metal complexes: D:Y.389, O.38

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

ACT.2: 7 residues within 4Å: Chain A: V.143, A.144, D.155, V.156, F.181, I.192, V.195 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.143, A:F.181, A:I.192, A:V.195 Hydrogen bonds: A:V.156 Water bridges: A:D.155, A:D.155 ACT.3: 9 residues within 4Å: Chain A: N.176, G.233, N.234, P.237, H.242, M.243, K.273, A.274, I.558 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.237, A:I.558 Hydrogen bonds: A:N.176 Water bridges: A:N.234, A:N.234, A:N.234, A:D.244, A:D.244 ACT.11: 7 residues within 4Å: Chain B: V.143, A.144, D.155, V.156, F.181, I.192, V.195 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.143, B:F.181, B:I.192, B:V.195 Water bridges: B:V.156, B:V.156 ACT.12: 8 residues within 4Å: Chain B: N.176, N.234, P.237, H.242, M.243, K.273, A.274, I.558 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.237, B:I.558 Hydrogen bonds: B:N.176, B:D.244 Water bridges: B:K.273 ACT.21: 7 residues within 4Å: Chain C: V.143, A.144, D.155, V.156, F.181, I.192, V.195 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.143, C:F.181, C:I.192, C:V.195 Hydrogen bonds: C:V.156 ACT.22: 8 residues within 4Å: Chain C: N.176, N.234, P.237, H.242, M.243, K.273, A.274, I.558 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:P.237, C:I.558 Hydrogen bonds: C:N.176 Water bridges: C:N.234, C:N.234, C:D.244, C:D.244 ACT.32: 7 residues within 4Å: Chain D: V.143, A.144, D.155, V.156, F.181, I.192, V.195 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.143, D:F.181, D:I.192, D:V.195 Hydrogen bonds: D:V.156 ACT.33: 9 residues within 4Å: Chain D: N.176, N.234, P.237, H.242, M.243, D.244, K.273, A.274, I.558 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:P.237, D:I.558 Hydrogen bonds: D:N.176, D:N.234, D:D.244 Water bridges: D:N.234, D:N.234

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 5 residues within 4Å: Chain A: T.600, D.611, Q.612, A.616, A.621 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.618 Water bridges: A:K.287, A:N.288, A:A.616 PGE.14: 3 residues within 4Å: Chain B: T.600, Q.612, A.621 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.288, B:Q.612 PGE.34: 7 residues within 4Å: Chain A: F.635, A.640, S.651, Q.652, R.659 Chain D: Q.652, R.659 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.659, D:R.659, A:Q.652, A:R.659 Water bridges: D:S.651, D:S.651

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 3 residues within 4Å: Chain A: D.477, T.546, Y.547 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.547 PEG.24: 2 residues within 4Å: Chain C: Y.323, G.324 No protein-ligand interaction detected (PLIP) PEG.25: 4 residues within 4Å: Chain C: T.600, D.611, Q.612, A.621 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.288, C:K.598 PEG.26: 1 residues within 4Å: Chain C: V.552 No protein-ligand interaction detected (PLIP)

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: E.337, F.338, L.484, N.551, V.552 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.551, A:V.552 EDO.7: 3 residues within 4Å: Chain A: Y.438, L.439, K.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.441 Water bridges: A:K.441 EDO.15: 3 residues within 4Å: Chain B: Y.438, L.439, K.441 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.441 EDO.16: 4 residues within 4Å: Chain B: F.338, L.484, N.551, V.552 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.552 Water bridges: B:N.551 EDO.27: 6 residues within 4Å: Chain C: R.409, P.410, V.411, S.412, G.413, V.414 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.410, C:G.413, C:V.414 Water bridges: C:R.409 EDO.28: 4 residues within 4Å: Chain C: S.198, D.200, N.201 Chain D: I.431 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C Water bridges: B:Q.294, D:H.432 Hydrogen bonds: C:N.201 EDO.29: 2 residues within 4Å: Chain C: T.546, Y.547 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Y.547 EDO.35: 2 residues within 4Å: Chain D: R.659, I.677 No protein-ligand interaction detected (PLIP) EDO.36: 3 residues within 4Å: Chain D: Y.438, L.439, K.441 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.441 EDO.37: 4 residues within 4Å: Chain D: Q.321, F.325, D.326, T.474 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.321, D:T.474

4 x O: OXYGEN ATOM(Non-covalent)

O.8: 5 residues within 4Å: Chain A: V.101, H.102, F.188, Y.389 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.102 O.17: 4 residues within 4Å: Chain B: V.101, H.102, F.188 Ligands: HEM.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.389 O.30: 4 residues within 4Å: Chain C: V.101, H.102, F.188 Ligands: HEM.20 No protein-ligand interaction detected (PLIP) O.38: 4 residues within 4Å: Chain D: V.101, H.102, F.188 Ligands: HEM.31 No protein-ligand interaction detected (PLIP)

5 x EOH: ETHANOL(Non-functional Binders)

EOH.9: 3 residues within 4Å: Chain A: E.317, G.460, R.461 No protein-ligand interaction detected (PLIP) EOH.18: 3 residues within 4Å: Chain B: R.252, E.317, G.460 No protein-ligand interaction detected (PLIP) EOH.19: 5 residues within 4Å: Chain B: Y.658, R.659, G.678, V.679 Ligands: 1PE.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.658, B:V.679 Hydrogen bonds: B:R.659 EOH.39: 4 residues within 4Å: Chain B: E.45, V.46 Chain D: R.409, W.426 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:V.46 Hydrogen bonds: D:R.409 EOH.40: 3 residues within 4Å: Chain D: T.480, H.549, N.551 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.549

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

1PE.13: 11 residues within 4Å: Chain B: S.651, Q.652, T.655, R.659 Chain C: F.635, M.641, S.651, Q.652, T.655, R.659 Ligands: EOH.19 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.651, B:R.659, B:R.659, C:S.651, C:R.659

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.23: 5 residues within 4Å: Chain C: W.118, L.341, Q.342, V.343, L.344 1 PLIP interactions: 1 interactions with chain C Water bridges: C:V.343

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

2019-05-01

Peptides

Catalase-3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase-3

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