MolNFT v1 · #140639 · protein
The crystal structure of staphylococcus aureus cnta in complex with staphylopine and cobalt
5YHE · Nickel ABC transporter substrate-binding protein: “The crystal structure of staphylococcus aureus cnta in complex with staphylopine and cobalt”. X-ray diffraction, 3 ligands (8UX, CO, CL), 6 pockets (best druggability 0.78). MolNFT…
- PDB
- 5YHE
- Type
- protein
- Length
- 1,013 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel ABC transporter substrate-binding protein
- UniProt
- A0A068A9N4
- Ligands
- 8UX, CO, CL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel ABC transporter substrate-binding protein | protein | 506 | 31% helix, 26% strand | A0A068A9N4 |
| B | Nickel ABC transporter substrate-binding protein | protein | 507 | 31% helix, 26% strand | A0A068A9N4 |
Ligands and binding sites
- 8UX · (2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.78 | 0.81 | 98 | ACT |
| 2 | 257 | 0.77 | 0.90 | 45 | 8UX, CO |
| 3 | 288 | 0.75 | 0.87 | 43 | 8UX, CO |
| 4 | 503 | 0.71 | 0.80 | 72 | ACT |
| 5 | 501 | 0.69 | 0.80 | 74 | empty |
Interfaces
1 interface between chains.
- A–B · 730 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5YHE · The crystal structure of Staphylococcus aureus CntA in complex with staphylopine and… · 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 A0A068A9N4
- Elsewhere: RCSB PDB 5YHE · PDBe 5YHE · UniProt A0A068A9N4
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