SMTL ID : 1r3v.1

Uroporphyrinogen Decarboxylase single mutant D86E in complex with coproporphyrinogen-I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x 1CP: COPROPORPHYRINOGEN I(Non-covalent)

1CP.1: 20 residues within 4Å: Chain A: R.37, A.39, R.41, F.46, F.55, I.82, F.84, S.85, E.86, I.87, M.100, P.106, F.154, Y.164, G.170, F.217, S.219, H.220, H.339 Ligands: BME.2 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:F.46, A:F.55, A:F.55, A:F.84, A:F.84, A:I.87, A:I.87, A:F.154, A:Y.164, A:F.217 Hydrogen bonds: A:R.37, A:E.86, A:E.86, A:E.86, A:E.86, A:Y.164, A:Y.164, A:S.219, A:S.219 Water bridges: A:R.37, A:R.37, A:R.37, A:A.39, A:R.50, A:G.105, A:S.171 Salt bridges: A:R.37, A:R.41, A:H.220, A:H.339 pi-Stacking: A:F.55 1CP.3: 20 residues within 4Å: Chain B: R.37, A.39, R.41, F.46, F.55, I.82, F.84, S.85, E.86, I.87, M.100, P.106, F.154, Y.164, G.170, F.217, S.219, H.220, H.339 Ligands: BME.4 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:F.46, B:F.55, B:F.55, B:F.84, B:F.84, B:I.87, B:I.87, B:F.154, B:Y.164, B:F.217 Hydrogen bonds: B:R.37, B:E.86, B:E.86, B:E.86, B:E.86, B:Y.164, B:Y.164, B:S.219, B:S.219 Water bridges: B:R.37, B:R.37, B:R.37, B:A.39, B:R.50, B:G.105, B:S.171 Salt bridges: B:R.37, B:R.41, B:H.220, B:H.339 pi-Stacking: B:F.55

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 2 residues within 4Å: Chain A: R.37 Ligands: 1CP.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.41, A:R.41 BME.4: 2 residues within 4Å: Chain B: R.37 Ligands: 1CP.3 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.41, B:R.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, J.D. et al., Structural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase. Embo J. (2003)

Release Date

2003-12-09

Peptides

Uroporphyrinogen Decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Uroporphyrinogen Decarboxylase