SMTL ID : 7vju.1

Crystal Structure of terephthalate dioxygenase from Comamonas testosteroni KF1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

hetero-3-3-mer

Ligands

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 9 residues within 4Å: Chain A: C.82, H.84, R.85, A.87, C.102, Y.104, H.105, A.106, W.107 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.82, A:H.84, A:C.102, A:H.105 FES.10: 9 residues within 4Å: Chain C: C.82, H.84, R.85, A.87, C.102, Y.104, H.105, A.106, W.107 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.82, C:H.84, C:C.102, C:H.105 FES.19: 10 residues within 4Å: Chain E: C.82, H.84, R.85, G.86, A.87, C.102, Y.104, H.105, A.106, W.107 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.82, E:H.84, E:C.102, E:H.105

3 x FE2: FE (II) ION(Non-covalent)

FE2.2: 3 residues within 4Å: Chain A: H.210, H.215, D.356 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.210, A:H.215, A:D.356, H2O.6, H2O.7 FE2.11: 3 residues within 4Å: Chain C: H.210, H.215, D.356 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.210, C:H.215, C:D.356, C:D.356, H2O.17 FE2.20: 3 residues within 4Å: Chain E: H.210, H.215, D.356 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.210, E:H.215, E:D.356, H2O.31, H2O.32

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 9 residues within 4Å: Chain A: T.57, T.58, F.59, P.64, I.65, N.80, A.90, L.91, K.93 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.58, A:I.65, A:I.65, A:N.80 Water bridges: C:R.365 PEG.4: 7 residues within 4Å: Chain A: Y.42, L.43, R.56, T.57, T.58, K.93, T.324 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.56, A:T.57, A:T.324, A:T.324 Water bridges: A:R.189, A:Q.310 PEG.9: 6 residues within 4Å: Chain A: G.128, G.129, P.131 Chain C: G.380, G.381, D.382 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.128, C:D.382 PEG.12: 12 residues within 4Å: Chain C: T.57, T.58, F.59, P.64, I.65, N.80, A.90, L.91, E.92, K.93 Chain E: R.365 Chain F: H.109 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:T.57, C:I.65, C:I.65, C:N.80, E:R.365 PEG.21: 9 residues within 4Å: Chain B: H.109 Chain E: T.57, T.58, F.59, P.64, I.65, N.80, L.91, K.93 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.58, E:I.65, E:I.65, E:N.80 PEG.22: 9 residues within 4Å: Chain E: I.89, A.90, L.91, E.92, T.97, S.99, F.100, Q.101, V.103 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.91, E:Q.101 PEG.26: 6 residues within 4Å: Chain F: F.10, T.28, F.29, K.131, L.132, R.133 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.28, F:K.131 Water bridges: F:A.9, F:K.131

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: I.89, A.90, L.91, E.92, T.97, S.99, Q.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.91, A:T.97, A:T.97, A:Q.101 GOL.16: 8 residues within 4Å: Chain D: E.114, V.115, F.116, V.145, T.146, D.147 Chain F: G.111, T.113 11 PLIP interactions: 2 interactions with chain C, 4 interactions with chain F, 5 interactions with chain D Water bridges: C:K.193, C:K.193, F:T.113, F:T.113, F:T.113 Hydrogen bonds: F:T.113, D:E.114, D:E.114, D:S.143, D:V.145, D:D.147 GOL.23: 8 residues within 4Å: Chain E: L.43, C.44, E.48, R.56, T.57, T.58, Q.310, N.322 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:R.56, E:R.56, E:T.57, E:T.324 Water bridges: E:L.45, E:Q.310, E:T.324

10 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 5 residues within 4Å: Chain A: G.380, G.381, H.383 Chain E: Q.127, G.128 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.381, E:G.128 Water bridges: A:S.387, A:E.388 Salt bridges: A:H.383 PO4.8: 2 residues within 4Å: Chain B: I.128, R.133 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.58 Water bridges: B:K.32 Salt bridges: B:K.32, B:R.133 PO4.13: 4 residues within 4Å: Chain C: Q.32, R.36, R.142 Chain E: N.372 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:Q.32, E:N.372 Water bridges: C:R.36, C:R.142, C:R.142 Salt bridges: C:R.36, C:R.142 PO4.14: 5 residues within 4Å: Chain C: E.92, K.93, S.94 Chain F: R.76, H.109 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:K.93, C:S.94 Water bridges: C:K.93, C:K.93, C:K.93, F:R.76 Salt bridges: C:K.93, F:H.109 PO4.15: 4 residues within 4Å: Chain A: V.124 Chain C: G.230, G.389, R.390 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.230, C:G.230, C:G.230, C:R.390 Salt bridges: C:R.390 PO4.17: 3 residues within 4Å: Chain D: K.32, I.128, R.133 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.58 Water bridges: D:K.32, D:K.32 Salt bridges: D:K.32, D:R.133 PO4.18: 5 residues within 4Å: Chain A: E.92, K.93, S.94 Chain D: R.76, H.109 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Salt bridges: D:R.76, D:H.109 Hydrogen bonds: A:K.93, A:S.94, A:S.94 PO4.24: 5 residues within 4Å: Chain B: R.76, H.109 Chain E: E.92, K.93, S.94 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:K.93, E:S.94, E:S.94 Water bridges: E:K.93 Salt bridges: B:R.76, B:H.109 PO4.25: 5 residues within 4Å: Chain A: G.369, N.372 Chain E: Q.32, R.36, R.142 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:Q.32, A:N.372, A:N.372 Water bridges: E:R.36, E:R.142, E:R.142 Salt bridges: E:R.36, E:R.142 PO4.27: 3 residues within 4Å: Chain F: K.32, I.128, R.133 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.58 Salt bridges: F:K.32, F:R.133

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

PG4.7: 4 residues within 4Å: Chain A: I.6, Q.7, W.8, M.411 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.7, A:Q.409

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mahto, J.K. et al., Structural Insights into Dihydroxylation of Terephthalate, a Product of Polyethylene Terephthalate Degradation. J.Bacteriol. (2022)

Release Date

2022-04-13

Peptides

Rieske (2Fe-2S) domain protein: ACE
Aromatic-ring-hydroxylating dioxygenase beta subunit: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Rieske (2Fe-2S) domain protein

Aromatic-ring-hydroxylating dioxygenase beta subunit