MolNFT v1 · #101184 · protein
Crystal structure of quee from burkholderia multivorans in complex with adomet and 6-carboxy-5,6,7,8-tetrahydropterin
4NJH · 7-carboxy-7-deazaguanine synthase: “Crystal structure of quee from burkholderia multivorans in complex with adomet and…”. X-ray diffraction, 5 ligands (SF4, SAM, 2K8), 4 pockets (best druggability 0.80). MolNFT v1 #101184 on…
- PDB
- 4NJH
- 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, 2K8, NA, PO4
- Pockets
- 4 · 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
- 2K8 · (6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridine-6-carboxylic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, 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
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 | 314 | 0.80 | 0.90 | 40 | SF4, SAM, 2K8, NA |
| 2 | 308 | 0.80 | 0.91 | 41 | SF4, SAM, 2K8, NA |
| 3 | 153 | 0.70 | 0.89 | 34 | empty |
| 4 | 51 | 0.31 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1260 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4NJH · Crystal Structure of QueE from Burkholderia multivorans in complex with AdoMet and… · 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 4NJH · PDBe 4NJH · UniProt A9AC61
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