SMTL ID : 5m7f.2 (1 other biounit)

Human porphobilinogen deaminase in complex with DPM cofactor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 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: 23 residues within 4Å: Chain A: L.34, Q.38, S.100, K.102, D.103, T.149, S.150, S.151, R.153, R.154, L.174, R.177, I.191, L.192, A.193, A.195, G.196, R.199, A.218, Q.221, G.222, C.265, S.266 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:L.34, A:A.193 Hydrogen bonds: A:Q.38, A:S.100, A:D.103, A:D.103, A:T.149, A:S.150, A:S.151, A:A.193, A:G.222 Water bridges: A:L.152, A:R.199, A:R.199, A:A.223, A:A.223 Salt bridges: A:K.102, A:K.102, A:K.102, A:R.153, A:R.154, A:R.154, A:R.154, A:R.177, A:R.199 pi-Cation interactions: A:K.102, A:K.102

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

SO4.2: 4 residues within 4Å: Chain A: H.304, P.306, A.307, Q.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.307, A:Q.308 Salt bridges: A:H.304 SO4.3: 4 residues within 4Å: Chain A: R.120, P.123, H.124, R.250 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.124, A:R.250 SO4.4: 4 residues within 4Å: Chain A: S.32, Q.33, N.173, N.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.33, A:N.173, A:N.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pluta, P. et al., Structural basis of pyrrole polymerization in human porphobilinogen deaminase. Biochim Biophys Acta Gen Subj (2018)

Release Date

2017-11-15

Peptides

Porphobilinogen deaminase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Porphobilinogen deaminase

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