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

Human porphobilinogen deaminase in complex with cofactor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x DPM: 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid(Covalent)

DPM.1: 16 residues within 4Å: Chain A: Q.36, S.98, K.100, D.101, S.148, S.149, R.151, R.152, R.175, L.190, A.191, R.197, A.216, Q.219, G.220, C.263 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:K.100, A:A.191 Hydrogen bonds: A:Q.36, A:D.101, A:D.101, A:S.148, A:S.149, A:A.191, A:G.220 Water bridges: A:L.99, A:T.147, A:R.151, A:R.175, A:R.197, A:R.197 Salt bridges: A:K.100, A:K.100, A:K.100, A:R.151, A:R.152, A:R.152, A:R.152, A:R.175, A:R.197 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.321, A:R.323, A:N.324 GOL.3: 4 residues within 4Å: Chain A: H.122, H.209, P.210, H.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.209, A:H.270

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
A

Porphobilinogen deaminase

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