SMTL ID : 5m6r.1 (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: 35 residues within 4Å: Chain A: L.58, Q.62, G.100, E.101, S.103, S.124, K.126, D.127, L.128, P.129, T.130, V.131, T.173, S.174, S.175, L.176, 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 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:E.101, A:K.126, A:A.217 Hydrogen bonds: A:Q.62, A:E.101, A:S.103, 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.174, A:S.175, A:S.175, A:A.217, A:V.243, A:V.243, A:Q.245, A:G.246, A:S.290, A:S.290 Water bridges: A:S.124, A:R.223 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

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

PO4.2: 7 residues within 4Å: Chain A: R.54, A.59, T.106, V.122, H.123, S.124, D.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.124, A:D.127 Salt bridges: A:R.54, A:H.123 PO4.3: 6 residues within 4Å: Chain A: K.71, P.75, G.76, L.77, Q.78, F.79 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.76, A:L.77, A:F.79 Salt bridges: A:K.71

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 8 residues within 4Å: Chain A: P.147, H.148, H.235, P.236, E.237, R.274, H.296, T.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.274, A:R.274

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
A

Porphobilinogen deaminase

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