SMTL ID : 8pnd.2 (1 other biounit)

The ES3 intermediate of hydroxymethylbilane synthase R167Q variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

ZWW.1: 27 residues within 4Å: Chain A: E.76, K.77, F.80, S.99, K.101, D.102, L.103, P.104, T.105, S.149, S.150, R.152, R.153, R.176, L.191, A.192, R.198, A.217, V.218, Q.220, G.221, L.257, G.262, G.263, C.264, S.265 Ligands: EDO.4 38 PLIP interactions: 38 interactions with chain A Hydrophobic interactions: A:E.76, A:F.80, A:T.105, A:A.192 Hydrogen bonds: A:Q.37, A:K.77, A:K.77, A:K.77, A:K.101, A:K.101, A:D.102, A:D.102, A:T.105, A:S.149, A:S.149, A:S.150, A:A.192, A:G.221, A:G.263, A:C.264, A:S.265 Water bridges: A:R.176, A:R.176, A:R.198, A:R.198, A:V.218 Salt bridges: A:K.77, A:K.101, A:K.101, A:K.101, A:R.152, A:R.153, A:R.153, A:R.153, A:R.176, A:R.198 pi-Cation interactions: A:K.101, A:K.101

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: H.123, H.210, P.211, H.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.271

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: N.174, L.177, W.201, R.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.174, A:R.204 EDO.4: 4 residues within 4Å: Chain A: G.263, C.264, V.268 Ligands: ZWW.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bustad, H.J. et al., One ring closer to a closure: the crystal structure of the ES 3 hydroxymethylbilane synthase intermediate. Febs J. (2024)

Release Date

2023-11-01

Peptides

Porphobilinogen deaminase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Porphobilinogen deaminase

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