SMTL ID : 4b2y.1

Probing the active center of catalase-phenol oxidase from Scytalidium thermophilum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: R.100, A.101, V.102, H.103, R.140, G.159, F.160, A.161, V.174, G.175, N.176, F.181, A.186, F.189, V.249, H.250, F.366, L.382, R.386, S.389, Y.390, T.393, Q.394, R.397 Chain C: D.93 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:R.100, A:H.103, A:A.161, A:V.174, A:N.176, A:F.181, A:F.189, A:F.189, A:F.189, A:V.249, A:V.249, A:F.366, A:L.382, A:L.382, A:R.386, A:Y.390 Hydrogen bonds: A:R.140, A:Q.394 Water bridges: A:A.101, A:A.161, A:F.366, A:R.397 Salt bridges: A:R.100, A:R.100, A:R.140, A:R.397 pi-Stacking: A:F.181, A:F.189 pi-Cation interactions: A:H.103, A:R.386 Metal complexes: A:Y.390 HEM.4: 25 residues within 4Å: Chain B: R.100, A.101, V.102, H.103, R.140, G.159, F.160, A.161, V.174, G.175, N.176, F.181, A.186, F.189, V.249, H.250, F.366, L.382, R.386, S.389, Y.390, T.393, Q.394, R.397 Chain D: D.93 32 PLIP interactions: 32 interactions with chain B, Hydrophobic interactions: B:A.101, B:H.103, B:A.161, B:V.174, B:N.176, B:F.181, B:F.181, B:A.186, B:F.189, B:F.189, B:F.189, B:F.189, B:V.249, B:V.249, B:F.366, B:L.382, B:L.382, B:R.386, B:Y.390 Hydrogen bonds: B:R.140, B:Q.394 Water bridges: B:T.393, B:R.397, B:R.397 Salt bridges: B:R.100, B:R.140, B:R.397 pi-Stacking: B:F.181, B:F.189 pi-Cation interactions: B:H.103, B:R.386 Metal complexes: B:Y.390 HEM.6: 25 residues within 4Å: Chain A: D.93 Chain C: R.100, A.101, V.102, H.103, R.140, G.159, F.160, A.161, V.174, G.175, N.176, F.181, A.186, F.189, V.249, H.250, F.366, L.382, R.386, S.389, Y.390, T.393, Q.394, R.397 28 PLIP interactions: 28 interactions with chain C, Hydrophobic interactions: C:R.100, C:H.103, C:A.161, C:V.174, C:N.176, C:F.181, C:F.189, C:F.189, C:F.189, C:F.189, C:V.249, C:V.249, C:F.366, C:L.382, C:L.382, C:R.386, C:Y.390 Hydrogen bonds: C:R.140, C:Q.394 Water bridges: C:F.366, C:T.393 Salt bridges: C:R.100, C:R.100, C:R.140, C:R.397 pi-Stacking: C:H.103, C:F.189 Metal complexes: C:Y.390 HEM.9: 24 residues within 4Å: Chain B: D.93 Chain D: R.100, V.102, H.103, R.140, G.159, F.160, A.161, V.174, G.175, N.176, F.181, A.186, F.189, V.249, H.250, F.366, L.382, R.386, S.389, Y.390, T.393, Q.394, R.397 28 PLIP interactions: 28 interactions with chain D, Hydrophobic interactions: D:H.103, D:A.161, D:V.174, D:N.176, D:F.181, D:F.189, D:F.189, D:F.189, D:V.249, D:V.249, D:F.366, D:L.382, D:L.382, D:R.386, D:Y.390 Hydrogen bonds: D:R.140, D:Q.394 Water bridges: D:A.101, D:F.366, D:R.397 Salt bridges: D:R.100, D:R.140, D:R.397 pi-Stacking: D:F.181, D:F.189 pi-Cation interactions: D:H.103, D:R.386 Metal complexes: D:Y.390

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

CA.2: 4 residues within 4Å: Chain A: R.199, H.211, D.212, S.213 No protein-ligand interaction detected (PLIP) CA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.5: 3 residues within 4Å: Chain B: R.199, H.211, S.213 No protein-ligand interaction detected (PLIP) CA.7: 4 residues within 4Å: Chain C: R.199, H.211, D.212, S.213 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain C: G.234, S.276, F.497 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.276 CA.10: 4 residues within 4Å: Chain D: R.199, H.211, D.212, S.213 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuzugullu, Y. et al., Investigating the Active Centre of the Scytalidium Thermophilum Catalase. Acta Crystallogr.,Sect.F (2013)

Release Date

2013-04-10

Peptides

CATALASE-PHENOL OXIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CATALASE-PHENOL OXIDASE