MolNFT v1 · #134834 · protein
Crystal structure of quee from bacillus subtilis with methionine bound
5TGS · 7-carboxy-7-deazaguanine synthase: “Crystal structure of quee from bacillus subtilis with methionine bound”. X-ray diffraction, 2 ligands (SF4, MET), 4 pockets (best druggability 0.79). MolNFT v1 #134834 on GenesisL1: 3D structure…
- PDB
- 5TGS
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7-carboxy-7-deazaguanine synthase
- EC
- 4.3.99.3
- UniProt
- O31677
- Ligands
- SF4, MET
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7-carboxy-7-deazaguanine synthase (EC 4.3.99.3) | protein | 230 | 38% helix, 23% strand | O31677 |
| B | 7-carboxy-7-deazaguanine synthase (EC 4.3.99.3) | protein | 231 | 39% helix, 23% strand | O31677 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- MET · Methionine · ligand · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.79 | 0.87 | 53 | SF4 |
| 2 | 480 | 0.77 | 0.85 | 52 | SF4, MET |
| 3 | 498 | 0.67 | 0.78 | 43 | empty |
| 4 | 50 | 0.39 | 0.82 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1506 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 5TGS · Crystal Structure of QueE from Bacillus subtilis with methionine bound · the same entry in another collection · chain A against A, TM-score 1.00
- O31677 · AlphaFold monomer V2.0 prediction for 7-carboxy-7-deazaguanine synthase (O31677) · a predicted model of the same protein · chain B 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 O31677
- Elsewhere: RCSB PDB 5TGS · PDBe 5TGS · UniProt O31677
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