SMTL ID : 3zj5.1

NEUROSPORA CRASSA CATALASE-3 EXPRESSED IN E. COLI, ORTHORHOMBIC FORM.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: P.362, E.364, L.511, V.579 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.511 Hydrogen bonds: A:E.364 EDO.2: 4 residues within 4Å: Chain A: R.279, E.344, G.487, R.488 No protein-ligand interaction detected (PLIP) EDO.7: 2 residues within 4Å: Chain B: Y.465, K.468 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.468 EDO.8: 3 residues within 4Å: Chain B: R.279, E.344, G.487 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.279 Water bridges: B:R.488, B:T.489 EDO.9: 2 residues within 4Å: Chain B: V.519, L.735 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.735 EDO.10: 2 residues within 4Å: Chain B: F.365, V.579 No protein-ligand interaction detected (PLIP) EDO.11: 1 residues within 4Å: Chain B: V.579 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.579 EDO.18: 3 residues within 4Å: Chain C: R.436, P.437, G.440 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.436, C:P.437, C:G.440 EDO.25: 3 residues within 4Å: Chain B: V.75 Chain D: R.436, W.453 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.436, D:R.436, D:W.453 Hydrophobic interactions: B:V.75 EDO.26: 3 residues within 4Å: Chain D: Y.685, R.686, I.704 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.685 EDO.27: 2 residues within 4Å: Chain D: Y.465, K.468 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:N.537 Hydrophobic interactions: D:Y.465, D:K.468

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

PG4.3: 2 residues within 4Å: Chain A: D.504, Y.574 No protein-ligand interaction detected (PLIP) PG4.4: 3 residues within 4Å: Chain A: Y.465, L.466, K.468 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.468 PG4.12: 7 residues within 4Å: Chain B: Q.679, T.682, R.686 Chain C: S.678, Q.679, T.682 Ligands: PG4.13 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Q.679, B:R.686, B:R.686 Hydrophobic interactions: B:T.682 PG4.13: 5 residues within 4Å: Chain B: F.662, A.667, S.678 Chain C: R.686 Ligands: PG4.12 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:A.667 Hydrogen bonds: C:R.686, C:R.686 PG4.14: 1 residues within 4Å: Chain B: Y.574 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.504 PG4.19: 2 residues within 4Å: Chain C: T.573, Y.574 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.504 PG4.20: 4 residues within 4Å: Chain C: A.349, Y.350, G.351, F.365 No protein-ligand interaction detected (PLIP) PG4.21: 4 residues within 4Å: Chain C: R.597, T.627, D.638, Q.639 No protein-ligand interaction detected (PLIP) PG4.22: 5 residues within 4Å: Chain C: S.515, L.516, V.579, T.580, N.587 No protein-ligand interaction detected (PLIP) PG4.23: 7 residues within 4Å: Chain C: W.145, I.148, P.367, L.368, Q.369, V.370, L.371 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.148 Water bridges: C:V.370 PG4.28: 2 residues within 4Å: Chain D: A.500, T.501 No protein-ligand interaction detected (PLIP) PG4.29: 3 residues within 4Å: Chain D: D.504, T.573, Y.574 No protein-ligand interaction detected (PLIP)

3 x AE3: 2-(2-ETHOXYETHOXY)ETHANOL(Non-covalent)

AE3.5: 3 residues within 4Å: Chain A: T.627, D.638, Q.639 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.315, A:R.597, A:A.643, A:A.643 AE3.15: 4 residues within 4Å: Chain B: T.627, D.638, Q.639, A.648 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.315 AE3.30: 6 residues within 4Å: Chain D: E.364, F.365, T.507, H.576, N.578, V.579 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.364 Hydrogen bonds: D:N.578

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

HEM.6: 27 residues within 4Å: Chain A: R.126, V.127, V.128, H.129, R.166, G.185, F.186, A.187, V.200, G.201, N.202, F.207, A.212, F.215, I.275, H.276, F.392, L.408, G.411, R.412, S.415, Y.416, T.419, Q.420, R.423 Chain D: L.115, D.119 30 PLIP interactions: 29 interactions with chain A, 1 interactions with chain D, Hydrophobic interactions: A:V.127, A:H.129, A:A.187, A:V.200, A:F.207, A:F.207, A:A.212, A:F.215, A:F.215, A:F.215, A:F.215, A:F.392, A:L.408, A:L.408, A:R.412, A:Y.416, A:Y.416, D:L.115 Hydrogen bonds: A:R.166, A:Q.420 Water bridges: A:F.392, A:T.419 Salt bridges: A:R.126, A:R.126, A:R.166, A:R.423 pi-Stacking: A:H.129, A:F.215 pi-Cation interactions: A:R.412 Metal complexes: A:Y.416 HEM.16: 26 residues within 4Å: Chain B: R.126, V.127, V.128, H.129, R.166, G.185, F.186, V.200, G.201, N.202, F.207, A.212, F.215, I.275, H.276, F.392, L.408, G.411, R.412, S.415, Y.416, T.419, Q.420, R.423 Chain C: L.115, D.119 31 PLIP interactions: 30 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:V.127, B:H.129, B:V.200, B:F.207, B:F.207, B:F.207, B:A.212, B:F.215, B:F.215, B:F.215, B:F.215, B:F.392, B:L.408, B:L.408, B:R.412, B:Y.416, B:Y.416, B:T.419, C:L.115 Hydrogen bonds: B:Q.420 Water bridges: B:V.127, B:R.166, B:T.419 Salt bridges: B:R.126, B:R.126, B:R.166, B:R.423 pi-Stacking: B:H.129, B:F.215 pi-Cation interactions: B:R.412 Metal complexes: B:Y.416 HEM.24: 27 residues within 4Å: Chain B: L.115, D.119 Chain C: R.126, V.127, V.128, H.129, R.166, G.185, F.186, A.187, V.200, G.201, N.202, F.207, A.212, F.215, I.275, H.276, F.392, L.408, G.411, R.412, S.415, Y.416, T.419, Q.420, R.423 33 PLIP interactions: 32 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:V.127, C:V.128, C:H.129, C:A.187, C:V.200, C:F.207, C:F.207, C:F.207, C:A.212, C:F.215, C:F.215, C:F.215, C:F.215, C:F.392, C:L.408, C:L.408, C:R.412, C:Y.416, C:Y.416, B:L.115 Hydrogen bonds: C:R.166, C:Q.420 Water bridges: C:V.127, C:A.187, C:T.419 Salt bridges: C:R.126, C:R.126, C:R.166, C:R.423 pi-Stacking: C:H.129, C:F.215 pi-Cation interactions: C:R.412 Metal complexes: C:Y.416 HEM.31: 27 residues within 4Å: Chain A: L.115, D.119 Chain D: R.126, V.127, V.128, H.129, R.166, G.185, F.186, A.187, V.200, G.201, N.202, F.207, A.212, F.215, I.275, H.276, F.392, L.408, G.411, R.412, S.415, Y.416, T.419, Q.420, R.423 32 PLIP interactions: 1 interactions with chain A, 31 interactions with chain D, Hydrophobic interactions: A:L.115, D:V.127, D:V.128, D:H.129, D:A.187, D:V.200, D:F.207, D:F.207, D:F.207, D:A.212, D:F.215, D:F.215, D:F.215, D:F.215, D:F.392, D:L.408, D:L.408, D:R.412, D:Y.416, D:Y.416 Hydrogen bonds: D:Q.420 Water bridges: D:V.127, D:R.166, D:T.419 Salt bridges: D:R.126, D:R.126, D:R.166, D:R.423 pi-Stacking: D:H.129, D:F.215 pi-Cation interactions: D:R.412 Metal complexes: D:Y.416

1 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.17: 4 residues within 4Å: Chain C: G.299, K.300, G.582, E.588 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.300, C:K.300, C:E.588 Water bridges: C:K.295, C:K.295, C:K.295, C:K.295, C:G.582 Salt bridges: C:K.295, C:K.300, C:K.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zarate-Romero, A. et al., Conformational Stability and Crystal Packing: Polymorphism in Neurospora Crassa Cat-3. Acta Crystallogr.,Sect.F (2013)

Release Date

2013-07-10

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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