MolNFT v1 · #140636 · protein
The crystal structure of staphylococcus aureus cnta in complex with staphylopine and nickel
5YH8 · Nickel ABC transporter substrate-binding protein: “The crystal structure of staphylococcus aureus cnta in complex with staphylopine and nickel”. X-ray diffraction, 2 ligands (8UX, NI), 3 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 5YH8
- Type
- protein
- Length
- 510 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel ABC transporter substrate-binding protein
- UniProt
- A0A068A9N4
- Ligands
- 8UX, NI
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel ABC transporter substrate-binding protein | protein | 510 | 31% helix, 23% 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 · chains A
- NI · Nickel (II) ion · metal · chains A
- GOL · Glycerol · additive · 9 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
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 | 263 | 0.77 | 0.89 | 39 | NI, 8UX, GOL |
| 2 | 599 | 0.71 | 0.79 | 78 | GOL, PEG |
| 3 | 88 | 0.60 | 0.89 | 19 | PEG |
Compared structures
- 5YH8 · 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 5YH8 · PDBe 5YH8 · UniProt A0A068A9N4
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