MolNFT v1 · #101187 · protein
Crystal structure of quee from burkholderia multivorans in complex with adomet, 7-carboxy-7-deazaguanine, and MG2+
4NJK · 7-carboxy-7-deazaguanine synthase: “Crystal structure of quee from burkholderia multivorans in complex with adomet, 7-carboxy-7-deazaguanine, and…”. X-ray diffraction, 6 ligands (SF4, SAM, 2KA), 3 pockets (best druggability 0.80).…
- PDB
- 4NJK
- Type
- protein
- Length
- 418 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
- A9AC61
- Ligands
- SF4, SAM, 2KA, MG, NA, PO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 7-carboxy-7-deazaguanine synthase (EC 4.3.99.3) | protein | 209 | 23% helix, 27% strand | A9AC61 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- 2KA · 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.80 | 0.91 | 39 | SF4, SAM, 2KA, MG |
| 2 | 299 | 0.80 | 0.91 | 41 | SF4, SAM, 2KA, MG |
| 3 | 152 | 0.71 | 0.90 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 1246 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4NJK · Crystal Structure of QueE from Burkholderia multivorans in complex with AdoMet… · the same entry in another collection · chain B against B, TM-score 1.00
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 A9AC61
- Elsewhere: RCSB PDB 4NJK · PDBe 4NJK · UniProt A9AC61
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