MolNFT v1 · #145371 · protein
Staphylococcus aureus dihydropteroate synthase (sadhps) F17L E208K double mutant structure
6CLV: “Staphylococcus aureus dihydropteroate synthase (sadhps) F17L E208K double mutant structure”. X-ray diffraction, 1 ligand (6MB), 7 pockets (best druggability 0.77). MolNFT v1 #145371 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6CLV
- Type
- protein
- Length
- 1,002 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- O05701
- Ligands
- 6MB
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 256 | 50% helix, 14% strand | O05701 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 249 | 50% helix, 15% strand | O05701 |
| C | Dihydropteroate synthase (EC 2.5.1.15) | protein | 257 | 49% helix, 14% strand | O05701 |
| D | Dihydropteroate synthase (EC 2.5.1.15) | protein | 240 | 53% helix, 14% strand | O05701 |
Ligands and binding sites
- 6MB · 4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl) methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.77 | 0.80 | 96 | 6MB |
| 2 | 249 | 0.65 | 0.83 | 47 | 6MB |
| 3 | 298 | 0.62 | 0.80 | 41 | 6MB |
| 4 | 75 | 0.33 | 0.75 | 18 | empty |
| 5 | 61 | 0.32 | 0.76 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1427 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1408 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 242 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 89 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 67 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CLV · Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure · the same entry in another collection · chain D against D, TM-score 1.00
- O05701 · AlphaFold monomer V2.0 prediction for dihydropteroate synthase (O05701) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 O05701
- Elsewhere: RCSB PDB 6CLV · PDBe 6CLV · UniProt O05701
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