SMTL ID : 3cb8.1

4Fe-4S-Pyruvate formate-lyase activating enzyme in complex with AdoMet and a peptide substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

monomer

Ligands

1 x VAL- SER- GLY- TYR- ALA- VAL: peptide substrate VSGYAV(Non-covalent)

VAL-SER-GLY-TYR-ALA-VAL.1: 10 residues within 4Å: Chain A: H.7, V.15, D.16, F.25, H.37, N.38, L.204, H.207, K.208 Ligands: SAM.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.15, A:F.25, A:H.37 Hydrogen bonds: A:D.16, A:N.38, A:N.38, A:H.207, A:K.208 Salt bridges: A:H.7, A:K.208

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: D.104, T.105, M.127, D.129 Ligands: SAM.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.127, A:D.129

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.3: 23 residues within 4Å: Chain A: Y.35, C.36, H.37, N.38, S.76, G.77, G.78, E.79, D.104, T.105, N.106, D.129, K.131, R.166, V.168, L.199, P.200, Y.201, H.202 Ligands: VAL-SER-GLY-TYR-ALA-VAL.1, VAL-SER-GLY-TYR-ALA-VAL.1, NA.2, SF4.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.35, A:Y.35, A:H.37, A:E.79, A:E.79, A:T.105, A:N.106, A:K.131, A:K.131, A:R.166, A:H.202 Salt bridges: A:D.104, A:K.131 pi-Stacking: A:Y.35, A:H.37 pi-Cation interactions: A:H.202

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.4: 11 residues within 4Å: Chain A: C.29, M.31, C.33, C.36, T.41, W.42, G.77, G.78, N.106, K.131 Ligands: SAM.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.29, A:C.33, A:C.36, SAM.3

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 6 residues within 4Å: Chain A: V.15, D.16, G.17, W.164, R.166, E.197 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.17, A:R.166 FMT.6: 3 residues within 4Å: Chain A: R.111, D.113 Ligands: FMT.8 No protein-ligand interaction detected (PLIP) FMT.7: 5 residues within 4Å: Chain A: F.108, V.109, R.110, R.111 Ligands: FMT.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.110, A:R.110, A:R.111 FMT.8: 4 residues within 4Å: Chain A: R.110, R.111 Ligands: FMT.6, FMT.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vey, J.L. et al., Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-10-28

Peptides

Pyruvate formate-lyase 1-activating enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pyruvate formate-lyase 1-activating enzyme

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