SMTL ID : 6bpw.1

Crystal structure of ferrous form of the Cl2-Tyr157 human cysteine dioxygenase with both uncrosslinked and crosslinked cofactor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

monomer

Ligands

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

FE2.1: 4 residues within 4Å: Chain A: H.86, H.88, H.140, X.157 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.86, A:H.88, A:H.140, H2O.1, H2O.1, H2O.3

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: T.180, F.181, K.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.181, A:F.181, A:K.184 GOL.3: 5 residues within 4Å: Chain A: P.44, L.98, Q.99, E.127, N.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.127, A:N.128 Water bridges: A:G.100 GOL.4: 2 residues within 4Å: Chain A: L.7, E.32 No protein-ligand interaction detected (PLIP) GOL.5: 4 residues within 4Å: Chain A: R.57, Y.58, S.83, S.84 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.57, A:S.84, A:S.84 Water bridges: A:Y.58, A:Y.58, A:R.60, A:H.86 GOL.6: 3 residues within 4Å: Chain A: N.90, S.91, H.92 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.91 Water bridges: A:H.92, A:N.134, A:S.136 GOL.7: 2 residues within 4Å: Chain A: R.10, D.14 No protein-ligand interaction detected (PLIP)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 4 residues within 4Å: Chain A: Q.34, R.123, A.131, Y.132 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.34, A:Q.34, A:Y.132 Water bridges: A:R.123, A:R.123 Salt bridges: A:R.123 SO4.9: 3 residues within 4Å: Chain A: K.119, R.141, Q.169 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.169 Water bridges: A:K.103, A:K.119 Salt bridges: A:K.103, A:K.119, A:R.141 SO4.10: 3 residues within 4Å: Chain A: G.172, H.173, K.174 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.174 Water bridges: A:K.174 Salt bridges: A:H.173, A:K.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Cleavage of a carbon-fluorine bond by an engineered cysteine dioxygenase. Nat. Chem. Biol. (2018)

Release Date

2018-07-04

Peptides

Cysteine dioxygenase type 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cysteine dioxygenase type 1

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