SMTL ID : 4wsh.1

Crystal structure of Probable Uroporphyrinogen decarboxylase (UPD) (URO-D) from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: D.283, I.284, N.300, R.319 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: D.283, I.284, N.300, R.319 Ligand excluded by PLIP

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

SO4.2: 7 residues within 4Å: Chain A: P.25, V.26, G.327, T.328, Y.361, H.362, G.363 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.26, A:T.328, A:G.363 Salt bridges: A:H.362 SO4.3: 4 residues within 4Å: Chain A: R.35, G.38, R.39, P.340 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.39 Water bridges: A:R.35, A:R.35 Salt bridges: A:R.35, A:R.39 SO4.4: 4 residues within 4Å: Chain A: L.243, I.244, R.245, E.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.245, A:E.246 SO4.5: 4 residues within 4Å: Chain A: S.114, L.115, N.183, A.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.115, A:N.183 Water bridges: A:A.116 SO4.6: 5 residues within 4Å: Chain A: M.9, L.22, Q.24, R.250, R.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.24, A:R.251 SO4.7: 2 residues within 4Å: Chain A: N.14, R.16 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.14, A:N.14 Salt bridges: A:R.16 SO4.8: 3 residues within 4Å: Chain A: R.35, H.336, G.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.337 Salt bridges: A:R.35, A:H.336 SO4.10: 7 residues within 4Å: Chain B: P.25, V.26, G.327, T.328, Y.361, H.362, G.363 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.26, B:T.328, B:G.363 Water bridges: B:V.26 Salt bridges: B:H.362 SO4.11: 4 residues within 4Å: Chain B: R.35, G.38, R.39, P.340 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.39 Water bridges: B:R.35, B:R.35, B:R.39, B:Y.44, B:R.48, B:R.48, B:I.338, B:I.338 Salt bridges: B:R.35, B:R.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of Probable Uroporphyrinogen decarboxylase (UPD) (URO-D) from Pseudomonas aeruginosa. to be published

Release Date

2014-11-19

Peptides

Uroporphyrinogen decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uroporphyrinogen decarboxylase