SMTL ID : 6vi7.1

Probing extradiol dioxygenase mechanism in NAD(+) biosynthesis by viewing reaction cycle intermediates - a substrate bidentately bound structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-dimer

Ligands

2 x 3HA: 3-HYDROXYANTHRANILIC ACID(Non-covalent)

3HA.1: 13 residues within 4Å: Chain A: V.46, N.48, V.62, R.68, H.72, E.78, F.80, H.116, P.118, R.120, E.131, I.163 Ligands: FE2.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.46, A:P.118, A:I.163 Hydrogen bonds: A:H.72 Salt bridges: A:R.120 pi-Cation interactions: A:R.68 3HA.5: 13 residues within 4Å: Chain B: V.46, N.48, V.62, R.68, H.72, E.78, F.80, H.116, P.118, R.120, E.131, I.163 Ligands: FE2.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.46, B:P.118, B:I.163 Hydrogen bonds: B:E.131 Salt bridges: B:R.120 pi-Cation interactions: B:R.68

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

FE2.2: 5 residues within 4Å: Chain A: H.72, E.78, H.116, E.131 Ligands: 3HA.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.72, A:E.78, A:E.78, A:H.116 FE2.3: 4 residues within 4Å: Chain A: C.146, C.149, C.183, C.186 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.146, A:C.149, A:C.183, A:C.186 FE2.6: 5 residues within 4Å: Chain B: H.72, E.78, H.116, E.131 Ligands: 3HA.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.72, B:E.78, B:E.78, B:H.116 FE2.7: 4 residues within 4Å: Chain B: C.146, C.149, C.183, C.186 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.146, B:C.149, B:C.183, B:C.186

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 6 residues within 4Å: Chain A: V.153, H.154, D.179, K.180, R.182, P.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.153, A:K.180 TRS.8: 6 residues within 4Å: Chain B: V.153, H.154, D.179, K.180, R.182, P.184 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.153, B:H.154, B:K.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-02-12

Peptides

3-hydroxyanthranilate 3,4-dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3-hydroxyanthranilate 3,4-dioxygenase

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