SMTL ID : 6edh.1

Taurine:2OG dioxygenase (TauD) bound to the vanadyl ion, taurine, and succinate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-tetramer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: L.114, T.126, W.240, A.257, R.266 Ligands: VVO.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.114, A:A.257 Hydrogen bonds: A:T.126, A:T.126 Salt bridges: A:R.266 ACT.3: 6 residues within 4Å: Chain B: L.114, T.126, W.240, A.257, R.266 Ligands: VVO.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.114, B:A.257 Hydrogen bonds: B:T.126, B:T.126 Salt bridges: B:R.266

4 x VVO: oxovanadium(2+)(Non-covalent)

VVO.2: 5 residues within 4Å: Chain A: N.95, H.99, D.101, H.255 Ligands: ACT.1 No protein-ligand interaction detected (PLIP) VVO.4: 5 residues within 4Å: Chain B: N.95, H.99, D.101, H.255 Ligands: ACT.3 No protein-ligand interaction detected (PLIP) VVO.6: 7 residues within 4Å: Chain C: N.95, H.99, D.101, H.255, R.270 Ligands: SIN.5, TAU.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.270 VVO.12: 7 residues within 4Å: Chain D: N.95, H.99, D.101, H.255, R.270 Ligands: SIN.11, TAU.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.270

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.5: 12 residues within 4Å: Chain C: L.85, N.95, H.99, D.101, L.114, T.126, H.255, A.257, R.266, M.268, R.270 Ligands: VVO.6 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.85, C:L.114, C:A.257 Hydrogen bonds: C:T.126 Water bridges: C:R.266 Salt bridges: C:H.99, C:H.255, C:R.266, C:R.270 SIN.11: 12 residues within 4Å: Chain D: L.85, N.95, H.99, D.101, L.114, T.126, H.255, A.257, R.266, M.268, R.270 Ligands: VVO.12 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.85, D:L.114, D:A.257 Hydrogen bonds: D:T.126 Water bridges: D:R.266 Salt bridges: D:H.99, D:H.255, D:R.266, D:R.270

2 x TAU: 2-AMINOETHANESULFONIC ACID(Non-covalent)

TAU.7: 11 residues within 4Å: Chain C: H.70, Y.73, D.94, N.95, D.101, V.102, F.104, F.159, F.206, R.270 Ligands: VVO.6 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.73, C:Y.73, C:V.102 Water bridges: C:N.97 Salt bridges: C:H.70, C:R.270 TAU.13: 11 residues within 4Å: Chain D: H.70, Y.73, D.94, N.95, D.101, V.102, F.104, F.159, F.206, R.270 Ligands: VVO.12 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.73, D:Y.73, D:V.102 Water bridges: D:N.97 Salt bridges: D:H.70, D:R.270

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

1PE.8: 6 residues within 4Å: Chain B: V.213 Chain C: E.136, A.137, L.138, S.139, R.143 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.143, C:R.143, B:V.211 1PE.14: 6 residues within 4Å: Chain A: V.213 Chain D: E.136, A.137, L.138, S.139, R.143 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.143, D:R.143, A:V.211

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

PEG.9: 5 residues within 4Å: Chain C: Y.135, V.140, R.143, Q.144, Y.280 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.143 Water bridges: C:Y.280 PEG.15: 5 residues within 4Å: Chain D: Y.135, V.140, R.143, Q.144, Y.280 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.143 Water bridges: D:Y.280

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

PG4.10: 7 residues within 4Å: Chain C: H.70, V.72, Y.73, P.74, H.75, D.80, R.173 No protein-ligand interaction detected (PLIP) PG4.16: 7 residues within 4Å: Chain D: H.70, V.72, Y.73, P.74, H.75, D.80, R.173 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davis, K.M. et al., Structure of a Ferryl Mimic in the Archetypal Iron(II)- and 2-(Oxo)-glutarate-Dependent Dioxygenase, TauD. Biochemistry (2019)

Release Date

2019-08-21

Peptides

Alpha-ketoglutarate-dependent taurine dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Alpha-ketoglutarate-dependent taurine dioxygenase

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