Research workbench
Crystal structure of quee from burkholderia multivorans in complex with adomet, 6-carboxy-5,6,7,8-tetrahydropterin, and MG2+
Analyse Crystal structure of quee from burkholderia multivorans in complex with adomet… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NJI
- 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, MG, NA, PO4
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 7-carboxy-7-deazaguanine synthase (EC 4.3.99.3) | protein | 209 | 25% helix, 26% 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
- 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 | 337 | 0.81 | 0.91 | 42 | SF4, SAM, 2K8, MG |
| 2 | 323 | 0.80 | 0.91 | 41 | SF4, SAM, 2K8, MG |
| 3 | 168 | 0.72 | 0.90 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 1263 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4NJI · Crystal Structure of QueE from Burkholderia multivorans in complex with AdoMet… · the same entry in another collection · chain A against A, 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 4NJI · PDBe 4NJI · UniProt A9AC61
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