SMTL ID : 5yem.1

CATPO mutant - T188F

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-tetramer

Ligands

10 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 4 residues within 4Å: Chain A: R.158, H.170, D.171, S.172 No protein-ligand interaction detected (PLIP) CA.2: 3 residues within 4Å: Chain A: F.416, T.417 Chain B: R.429 No protein-ligand interaction detected (PLIP) CA.3: 3 residues within 4Å: Chain A: R.429 Chain B: F.416, T.417 No protein-ligand interaction detected (PLIP) CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.6: 4 residues within 4Å: Chain B: R.158, H.170, D.171, S.172 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain B: G.193, S.235, F.456 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.235, H2O.38 CA.9: 4 residues within 4Å: Chain C: R.158, H.170, D.171, S.172 No protein-ligand interaction detected (PLIP) CA.10: 4 residues within 4Å: Chain C: G.193, S.235, F.456, V.519 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.235 CA.12: 4 residues within 4Å: Chain D: R.158, H.170, D.171, S.172 No protein-ligand interaction detected (PLIP) CA.13: 3 residues within 4Å: Chain D: G.193, S.235, F.456 No protein-ligand interaction detected (PLIP)

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

HEM.4: 24 residues within 4Å: Chain A: R.59, V.61, H.62, R.99, G.118, F.119, A.120, V.133, G.134, N.135, F.140, A.145, F.148, V.208, H.209, F.325, L.341, R.345, S.348, Y.349, T.352, Q.353, R.356 Chain C: D.52 32 PLIP interactions: 31 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:V.61, A:H.62, A:A.120, A:V.133, A:F.140, A:F.140, A:A.145, A:F.148, A:F.148, A:F.148, A:F.148, A:V.208, A:F.325, A:L.341, A:L.341, A:R.345, A:Y.349, A:Y.349 Hydrogen bonds: A:R.99, A:Q.353 Water bridges: A:A.60, A:A.120, A:F.325, A:R.356 Salt bridges: A:R.59, A:R.59, A:R.99, A:R.356 pi-Stacking: A:H.62, A:F.148 Metal complexes: A:Y.349, H2O.19 HEM.8: 24 residues within 4Å: Chain B: R.59, V.61, H.62, R.99, G.118, F.119, A.120, V.133, G.134, N.135, F.140, A.145, F.148, V.208, H.209, F.325, L.341, R.345, S.348, Y.349, T.352, Q.353, R.356 Chain D: D.52 33 PLIP interactions: 32 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:V.61, B:H.62, B:A.120, B:V.133, B:F.140, B:F.140, B:F.140, B:F.148, B:F.148, B:F.148, B:F.148, B:V.208, B:V.208, B:F.325, B:L.341, B:L.341, B:R.345, B:Y.349, B:Y.349 Hydrogen bonds: B:R.99, B:Q.353 Water bridges: B:A.120, B:T.352, B:T.352, B:R.356 Salt bridges: B:R.59, B:R.59, B:R.99, B:R.356 pi-Stacking: B:H.62, B:F.148 Metal complexes: B:Y.349, H2O.41 HEM.11: 25 residues within 4Å: Chain A: I.48, D.52 Chain C: R.59, V.61, H.62, R.99, G.118, F.119, A.120, V.133, G.134, N.135, F.140, A.145, F.148, V.208, H.209, F.325, L.341, R.345, S.348, Y.349, T.352, Q.353, R.356 36 PLIP interactions: 34 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: C:V.61, C:H.62, C:A.120, C:V.133, C:N.135, C:F.140, C:F.140, C:F.140, C:A.145, C:F.148, C:F.148, C:F.148, C:F.148, C:V.208, C:V.208, C:F.325, C:L.341, C:L.341, C:R.345, C:Y.349, C:Y.349, A:I.48 Hydrogen bonds: C:Q.353 Water bridges: C:A.60, C:R.99, C:A.120, C:F.325, C:R.356 Salt bridges: C:R.59, C:R.59, C:R.99, C:R.356 pi-Stacking: C:H.62, C:F.148 Metal complexes: C:Y.349, H2O.62 HEM.14: 24 residues within 4Å: Chain B: D.52 Chain D: R.59, V.61, H.62, R.99, G.118, F.119, A.120, V.133, G.134, N.135, F.140, A.145, F.148, V.208, H.209, F.325, L.341, R.345, S.348, Y.349, T.352, Q.353, R.356 30 PLIP interactions: 29 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:V.61, D:H.62, D:A.120, D:V.133, D:F.140, D:F.140, D:F.140, D:F.148, D:F.148, D:F.148, D:F.148, D:V.208, D:F.325, D:L.341, D:L.341, D:R.345, D:Y.349, D:Y.349 Hydrogen bonds: D:Q.353 Water bridges: D:A.60, D:V.323, D:R.356 Salt bridges: D:R.59, D:R.59, D:R.99, D:R.356 pi-Stacking: D:H.62, D:F.148 Metal complexes: D:Y.349, H2O.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuzugullu, Y.K. et al., Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase. Acta Crystallogr D Struct Biol (2024)

Release Date

2018-07-18

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase