SMTL ID : 5m6r.2 (1 other biounit)

Human porphobilinogen deaminase in complex with reaction intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 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: 34 residues within 4Å: Chain A: R.54, L.58, Q.62, L.104, F.105, S.124, K.126, D.127, L.128, P.129, T.130, V.131, T.173, S.174, S.175, R.177, R.178, R.201, I.215, L.216, A.217, A.219, G.220, R.223, A.242, V.243, Q.245, G.246, L.248, L.282, R.283, G.288, C.289, S.290 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:F.105, A:K.126, A:A.217 Hydrogen bonds: A:Q.62, A:S.124, A:K.126, A:D.127, A:D.127, A:D.127, A:T.130, A:T.130, A:S.174, A:S.175, A:S.175, A:A.217, A:V.243, A:V.243, A:G.246 Water bridges: A:C.289, A:S.290 Salt bridges: A:K.126, A:K.126, A:K.126, A:R.177, A:R.178, A:R.178, A:R.178, A:R.201, A:R.223 pi-Cation interactions: A:K.126, A:K.126

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: R.54, A.59, Q.62, H.123, S.124, D.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.62, A:S.124, A:S.124 Salt bridges: A:R.54, A:H.123

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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