Research workbench
4FE-4S-pyruvate formate-lyase activating enzyme in complex with adomet and a peptide substrate
Analyse 4FE-4S-pyruvate formate-lyase activating enzyme in complex with adomet and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CB8
- Type
- protein
- Length
- 250 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate formate-lyase 1-activating enzyme; Peptide substrate vsgyav
- EC
- 1.97.1.4
- UniProt
- P0A9N4
- Ligands
- SF4, SAM, NA
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate formate-lyase 1-activating enzyme (EC 1.97.1.4) | protein | 244 | 38% helix, 20% strand | P0A9N4 |
| B | Peptide substrate vsgyav | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- SAM · S-adenosylmethionine · ligand · chains A, B
- NA · Sodium ion · metal · chains A
- FMT · Formic acid · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.80 | 0.94 | 31 | SF4, SAM |
Interfaces
1 interface between chains.
- A–B · 443 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3CB8 · 4Fe-4S-Pyruvate formate-lyase activating enzyme in complex with AdoMet and a peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A9N4 · AlphaFold monomer V2.0 prediction for pyruvate formate-lyase 1-activating enzyme (P0A9N4) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A9N4
- Elsewhere: RCSB PDB 3CB8 · PDBe 3CB8 · UniProt P0A9N4
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