SMTL ID : 1j93.1

Crystal Structure and Substrate Binding Modeling of the Uroporphyrinogen-III Decarboxylase from Nicotiana tabacum: Implications for the Catalytic Mechanism

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: F.213, S.215, W.216, Y.252, S.254, H.330 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.215, A:Y.252, A:Y.252, A:S.254, A:S.254 Salt bridges: A:H.330 SO4.2: 1 residues within 4Å: Chain A: K.234 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.234 SO4.3: 4 residues within 4Å: Chain A: S.167, K.168, N.169, F.170 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.168, A:N.169, A:N.169, A:F.170 Water bridges: A:S.167, A:T.171 SO4.4: 4 residues within 4Å: Chain A: V.118, R.119, E.120, K.190 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.118, A:E.120 Water bridges: A:K.190 Salt bridges: A:R.119, A:K.190 SO4.5: 1 residues within 4Å: Chain A: R.138 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.138, A:A.203, A:A.203 Salt bridges: A:R.138 SO4.6: 6 residues within 4Å: Chain B: F.213, S.215, W.216, Y.252, S.254, H.330 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.215, B:Y.252, B:S.254, B:S.254 Salt bridges: B:H.330 SO4.7: 1 residues within 4Å: Chain B: K.234 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.234 SO4.8: 4 residues within 4Å: Chain B: S.167, K.168, N.169, F.170 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.168, B:N.169, B:N.169, B:F.170 Water bridges: B:S.167, B:T.171 SO4.9: 4 residues within 4Å: Chain B: V.118, R.119, E.120, K.190 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.118, B:E.120 Water bridges: B:K.190 Salt bridges: B:R.119, B:K.190 SO4.10: 1 residues within 4Å: Chain B: R.138 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.138, B:A.203, B:A.203 Salt bridges: B:R.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martins, B.M. et al., Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from Nicotiana tabacum. Implications for the catalytic mechanism. J.Biol.Chem. (2001)

Release Date

2001-10-17

Peptides

UROPORPHYRINOGEN DECARBOXYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UROPORPHYRINOGEN DECARBOXYLASE