SMTL ID : 7aak.2 (1 other biounit)

Human porphobilinogen deaminase R173W mutant crystallized in the ES2 intermediate state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x 7J8: 3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid(Covalent)

7J8.1: 24 residues within 4Å: Chain A: Q.36, S.77, S.98, K.100, D.101, L.102, P.103, T.104, S.148, S.149, R.151, R.152, L.190, A.191, R.197, A.216, V.217, Q.219, G.220, L.256, G.262, C.263, S.264 Ligands: GOL.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:A.191 Hydrogen bonds: A:S.77, A:K.100, A:D.101, A:D.101, A:T.104, A:S.149, A:A.191, A:R.197, A:G.220, A:S.264 Water bridges: A:V.105, A:L.150, A:L.150, A:R.151, A:A.221, A:A.221, A:R.253, A:S.264, A:S.264, A:S.264 Salt bridges: A:K.100, A:K.100, A:K.100, A:R.151, A:R.152, A:R.152 pi-Cation interactions: A:K.100, A:K.100

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: Q.231, L.234, D.235, T.321, A.322, R.323, N.324 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.231, A:D.235, A:T.321, A:R.323, A:N.324 Water bridges: A:D.235, A:G.238, A:D.309 GOL.3: 6 residues within 4Å: Chain A: A.216, V.217, L.256, V.265, V.267 Ligands: 7J8.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.217, A:V.267 Water bridges: A:S.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bustad, H.J. et al., Characterization of porphobilinogen deaminase mutants reveals that arginine-173 is crucial for polypyrrole elongation mechanism. Iscience (2021)

Release Date

2021-02-17

Peptides

Porphobilinogen deaminase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Porphobilinogen deaminase

Related Entries With Identical Sequence