SMTL ID : 6p5q.2 (2 other biounits)

X-ray structure of Fe(II)-soaked UndA bound to lauric acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x DAO: LAURIC ACID(Non-covalent)

DAO.1: 20 residues within 4Å: Chain A: V.82, Y.88, Y.104, G.108, V.111, V.112, F.115, E.148, W.155, L.181, I.205, E.206, T.209, W.212, W.237, H.241, M.283, F.286, L.287 Ligands: FE.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.111, A:F.115, A:F.115, A:I.205, A:M.283, A:F.286, A:F.286, A:L.287 Salt bridges: A:H.241 DAO.5: 20 residues within 4Å: Chain B: V.82, Y.88, Y.104, G.108, V.111, V.112, F.115, E.148, W.155, L.181, I.205, E.206, T.209, W.212, W.237, H.241, M.283, F.286, L.287 Ligands: FE.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.111, B:F.115, B:F.115, B:I.205, B:M.283, B:F.286, B:F.286, B:L.287 Salt bridges: B:H.241

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

FE.2: 3 residues within 4Å: Chain A: E.148, E.206, H.248 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.206, A:H.248, H2O.1, H2O.6 FE.3: 4 residues within 4Å: Chain A: E.148, H.151, H.241 Ligands: DAO.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.148, A:H.151, A:H.241, H2O.1 FE.6: 3 residues within 4Å: Chain B: E.148, E.206, H.248 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.206, B:H.248, H2O.7, H2O.12 FE.7: 4 residues within 4Å: Chain B: E.148, H.151, H.241 Ligands: DAO.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.148, B:H.151, B:H.241, H2O.7

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: R.146, L.149, N.150, Y.154, K.236, M.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.146, A:R.146, A:Y.154 GOL.8: 6 residues within 4Å: Chain B: R.146, L.149, N.150, Y.154, K.236, M.240 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.146, B:R.146, B:Y.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, B. et al., Substrate-Triggered Formation of a Peroxo-Fe2(III/III) Intermediate during Fatty Acid Decarboxylation by UndA. J.Am.Chem.Soc. (2019)

Release Date

2019-09-18

Peptides

UndA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UndA

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