SMTL ID : 6wf2.2 (1 other biounit)

Crystal structure of mouse SCD1 with a diiron center

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

monomer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: H.94, H.99, H.131, H.135, H.275 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.94, A:H.99, A:H.131, A:H.135, A:H.275 FE.2: 4 residues within 4Å: Chain A: H.134, H.243, H.272, H.276 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.134, A:H.243, A:H.272, A:H.276

1 x 3VV: S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)(Non-covalent)

3VV.3: 34 residues within 4Å: Chain A: N.49, Y.82, A.86, I.89, T.90, H.94, F.120, Q.121, N.122, E.126, W.127, R.129, D.130, H.131, W.158, L.159, V.161, R.162, K.163, V.167, K.168, G.171, G.172, R.189, Y.228, L.232, T.235, W.236, V.238, N.239, G.265, A.266, E.269, H.272 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:A.86, A:T.90, A:Q.121, A:W.127, A:W.158, A:V.238, A:V.238, A:A.266, A:E.269, A:E.269 Hydrogen bonds: A:N.49, A:N.122, A:R.129, A:R.129, A:R.129, A:K.163, A:K.163, A:R.189 Salt bridges: A:R.129, A:R.162, A:K.163, A:K.163, A:K.168 pi-Cation interactions: A:R.129, A:R.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, J. et al., Structure and Mechanism of a Unique Diiron Center in Mammalian Stearoyl-CoA Desaturase. J.Mol.Biol. (2020)

Release Date

2020-06-17

Peptides

Acyl-CoA desaturase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Membrane

We predict this structure to be a membrane protein.
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Acyl-CoA desaturase 1

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