SMTL ID : 7vn0.1

CATPO mutant - T188A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x HDD: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE(Non-covalent)(Covalent)

HDD.1: 26 residues within 4Å: Chain A: R.101, A.102, V.103, H.104, R.141, G.160, F.161, A.162, V.175, G.176, N.177, F.182, A.187, F.190, V.250, H.251, F.367, L.383, R.387, S.390, Y.391, T.394, Q.395, R.398 Chain C: F.93, D.94 31 PLIP interactions: 29 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: A:R.101, A:H.104, A:A.162, A:V.175, A:F.182, A:F.182, A:F.190, A:F.190, A:F.190, A:F.190, A:V.250, A:V.250, A:F.367, A:L.383, A:L.383, A:R.387, A:Y.391, A:Y.391, C:F.93 Hydrogen bonds: A:Q.395 Water bridges: A:A.162, A:R.398, A:R.398 Salt bridges: A:R.101, A:R.141, A:R.398 pi-Stacking: A:H.104, A:F.190 pi-Cation interactions: A:R.387 Metal complexes: A:Y.391, H2O.12 HDD.5: 25 residues within 4Å: Chain B: R.101, A.102, V.103, H.104, R.141, G.160, F.161, A.162, V.175, G.176, N.177, F.182, A.187, F.190, V.250, H.251, F.367, L.383, R.387, S.390, Y.391, T.394, Q.395, R.398 Chain D: D.94 30 PLIP interactions: 29 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:R.101, B:H.104, B:A.162, B:V.175, B:N.177, B:F.182, B:F.190, B:F.190, B:F.190, B:F.190, B:V.250, B:V.250, B:F.367, B:L.383, B:L.383, B:R.387, B:Y.391, B:Y.391 Hydrogen bonds: B:Q.395 Water bridges: B:A.162, B:R.398, B:R.398 Salt bridges: B:R.101, B:R.141, B:R.398 pi-Stacking: B:H.104, B:F.190 pi-Cation interactions: B:R.387 Metal complexes: B:Y.391, H2O.31 HDD.8: 25 residues within 4Å: Chain A: D.94 Chain C: R.101, A.102, V.103, H.104, R.141, G.160, F.161, A.162, V.175, G.176, N.177, F.182, A.187, F.190, V.250, H.251, F.367, L.383, R.387, S.390, Y.391, T.394, Q.395, R.398 30 PLIP interactions: 29 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:R.101, C:V.103, C:H.104, C:A.162, C:V.175, C:N.177, C:F.182, C:F.190, C:F.190, C:F.190, C:F.190, C:V.250, C:F.367, C:L.383, C:L.383, C:R.387, C:Y.391, C:Y.391 Hydrogen bonds: C:Q.395 Water bridges: C:A.162, C:R.398, C:R.398 Salt bridges: C:R.101, C:R.141, C:R.398 pi-Stacking: C:H.104, C:F.190 pi-Cation interactions: C:R.387 Metal complexes: C:Y.391, H2O.48 HDD.12: 25 residues within 4Å: Chain B: D.94 Chain D: R.101, A.102, V.103, H.104, R.141, G.160, F.161, A.162, V.175, G.176, N.177, F.182, A.187, F.190, V.250, H.251, F.367, L.383, R.387, S.390, Y.391, T.394, Q.395, R.398 31 PLIP interactions: 30 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:R.101, D:A.102, D:H.104, D:A.162, D:V.175, D:F.182, D:F.182, D:F.182, D:A.187, D:F.190, D:F.190, D:F.190, D:V.250, D:F.367, D:L.383, D:L.383, D:R.387, D:Y.391, D:Y.391 Hydrogen bonds: D:Q.395 Water bridges: D:A.162, D:R.398, D:R.398 Salt bridges: D:R.101, D:R.141, D:R.398 pi-Stacking: D:H.104, D:F.190 pi-Cation interactions: D:R.387 Metal complexes: D:Y.391, H2O.67

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

CA.2: 4 residues within 4Å: Chain A: R.200, H.212, D.213, S.214 No protein-ligand interaction detected (PLIP) CA.3: 3 residues within 4Å: Chain A: R.471 Chain B: F.458, T.459 No protein-ligand interaction detected (PLIP) CA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.6: 4 residues within 4Å: Chain B: R.200, H.212, D.213, S.214 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain B: G.235, S.277, F.498 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.277, H2O.32 CA.9: 4 residues within 4Å: Chain C: R.200, H.212, D.213, S.214 No protein-ligand interaction detected (PLIP) CA.10: 3 residues within 4Å: Chain C: G.235, S.277, F.498 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.277, H2O.47 CA.13: 4 residues within 4Å: Chain D: R.200, H.212, D.213, S.214 No protein-ligand interaction detected (PLIP) CA.14: 3 residues within 4Å: Chain D: G.235, S.277, F.498 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.277, H2O.70

1 x ALA: ALANINE(Covalent)

ALA.11: 2 residues within 4Å: Chain D: L.718, D.719 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuzugullu Karakus, Y. 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

2022-09-14

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase