Research workbench
The crystal structure of staphylococcus aureus cnta in complex with staphylopine and cobalt
Analyse The crystal structure of staphylococcus aureus cnta in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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