SMTL ID : 7wca.1

CATPO mutant - E484A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-tetramer

Ligands

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

CA.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 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: F.458, T.459 Chain B: R.471 No protein-ligand interaction detected (PLIP) CA.4: 3 residues within 4Å: Chain A: R.471 Chain B: F.458, T.459 No protein-ligand interaction detected (PLIP) CA.11: 4 residues within 4Å: Chain B: R.200, H.212, D.213, S.214 No protein-ligand interaction detected (PLIP) CA.12: 3 residues within 4Å: Chain B: G.235, S.277, F.498 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.277 CA.20: 4 residues within 4Å: Chain C: R.200, H.212, D.213, S.214 No protein-ligand interaction detected (PLIP) CA.21: 3 residues within 4Å: Chain C: G.235, S.277, F.498 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.277 CA.30: 4 residues within 4Å: Chain D: R.200, H.212, D.213, S.214 No protein-ligand interaction detected (PLIP) CA.31: 3 residues within 4Å: Chain D: G.235, S.277, F.498 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.277

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

HEM.5: 24 residues within 4Å: Chain A: R.101, 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: D.94 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:V.103, A:H.104, A:A.162, A:V.175, A:N.177, A:F.182, A:F.190, A:F.190, A:F.190, A:F.190, A:V.250, A:F.367, A:L.383, A:L.383, A:R.387, A:Y.391, A:Y.391 Hydrogen bonds: A:R.141, A:Q.395 Water bridges: A:A.102, 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 HEM.13: 24 residues within 4Å: Chain B: R.101, 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 33 PLIP interactions: 33 interactions with chain B, Hydrophobic interactions: B:V.103, B:H.104, B:A.162, B:V.175, B:N.177, B:F.182, B:F.182, 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:R.141, B:Q.395 Water bridges: B:A.102, B:A.162, B:R.398 Salt bridges: B:R.101, 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 HEM.22: 24 residues within 4Å: Chain A: D.94 Chain C: R.101, 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 29 PLIP interactions: 29 interactions with chain C, Hydrophobic interactions: 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.102, C:R.398, C:R.398 Salt bridges: C:R.101, 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 HEM.32: 23 residues within 4Å: Chain B: D.94 Chain D: R.101, V.103, H.104, R.141, G.160, F.161, 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: 30 interactions with chain D, Hydrophobic interactions: D:V.103, D:H.104, D:V.175, D:N.177, D:F.182, D:F.182, D:F.190, D:F.190, D:F.190, D:F.190, D:V.250, D:V.250, D:F.367, D:L.383, D:L.383, D:R.387, D:Y.391, D:Y.391, D:Y.391 Hydrogen bonds: D:Q.395 Water bridges: D:A.102, 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

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

1PE.6: 7 residues within 4Å: Chain A: S.304, G.305, N.306, T.568, K.570, K.598, G.600 Ligand excluded by PLIP 1PE.7: 8 residues within 4Å: Chain A: A.47, Y.48, E.49, V.50 Chain D: Y.48, M.411, F.428 Ligands: 1PE.35 Ligand excluded by PLIP 1PE.8: 7 residues within 4Å: Chain A: R.431, K.433 Chain B: D.202 Chain D: W.299, E.303, P.355, T.356 Ligand excluded by PLIP 1PE.9: 8 residues within 4Å: Chain A: S.220, Q.221, N.518, T.521, Q.522 Chain B: N.439, S.443, G.444 Ligand excluded by PLIP 1PE.10: 1 residues within 4Å: Chain A: N.452 Ligand excluded by PLIP 1PE.14: 5 residues within 4Å: Chain B: T.521, G.541, A.542, P.543, D.544 Ligand excluded by PLIP 1PE.15: 8 residues within 4Å: Chain B: Y.48, M.411 Chain C: A.47, Y.48, V.50, M.411, F.428 Ligands: 1PE.27 Ligand excluded by PLIP 1PE.16: 9 residues within 4Å: Chain A: D.202 Chain B: H.430, R.431, K.433 Chain C: W.299, E.303, N.354, P.355, T.356 Ligand excluded by PLIP 1PE.17: 10 residues within 4Å: Chain B: E.339, Y.340, D.479, S.482, L.486, T.548, Y.549, H.551, N.553, K.554 Ligand excluded by PLIP 1PE.18: 5 residues within 4Å: Chain B: T.642, A.643, S.644 Chain D: D.714, R.715 Ligand excluded by PLIP 1PE.19: 6 residues within 4Å: Chain B: S.220, Q.221, W.481, Q.522, R.525, D.546 Ligand excluded by PLIP 1PE.23: 5 residues within 4Å: Chain C: G.305, N.306, K.570, K.598, G.600 Ligand excluded by PLIP 1PE.24: 6 residues within 4Å: Chain C: T.115, S.116, Y.117, T.132, G.133, L.348 Ligand excluded by PLIP 1PE.25: 5 residues within 4Å: Chain C: I.302, E.303, G.305, D.352, R.353 Ligand excluded by PLIP 1PE.26: 8 residues within 4Å: Chain C: N.439, T.440, S.443, G.444 Chain D: S.220, Q.221, N.518, Q.522 Ligand excluded by PLIP 1PE.27: 8 residues within 4Å: Chain B: V.50, D.51 Chain C: M.411, V.414, P.415, I.416, H.417 Ligands: 1PE.15 Ligand excluded by PLIP 1PE.28: 3 residues within 4Å: Chain C: K.270, L.343, K.345 Ligand excluded by PLIP 1PE.29: 7 residues within 4Å: Chain C: S.220, Q.221, P.223, W.481, N.518, Q.522, R.525 Ligand excluded by PLIP 1PE.33: 3 residues within 4Å: Chain D: P.543, D.544, D.546 Ligand excluded by PLIP 1PE.34: 5 residues within 4Å: Chain D: I.302, E.303, G.305, D.352, R.353 Ligand excluded by PLIP 1PE.35: 10 residues within 4Å: Chain A: V.50, D.51 Chain D: M.411, P.412, R.413, V.414, P.415, I.416, H.417 Ligands: 1PE.7 Ligand excluded by PLIP 1PE.36: 6 residues within 4Å: Chain D: Y.340, L.486, T.548, Y.549, H.551, N.553 Ligand excluded by PLIP 1PE.37: 6 residues within 4Å: Chain D: G.305, N.306, K.570, K.598, D.599, G.600 Ligand excluded by PLIP 1PE.38: 4 residues within 4Å: Chain D: K.263, I.316, V.317, D.318 Ligand excluded by 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

2022-12-21

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase