MolNFT v1 · #138841 · protein
Crystal structure of the second DNA-binding protein under starvation from mycobacterium smegmatis soaked with iron in the ratio of 480 iron atoms per dodecamer
5WW8 · Putative starvation-induced DNA protecting PROTEIN/FERRITIN…: “Crystal structure of the second DNA-binding protein under starvation from mycobacterium smegmatis soaked with…”. X-ray diffraction, 4 ligands (FE, FE2, MG), 4 pockets…
- PDB
- 5WW8
- Type
- protein
- Length
- 641 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps
- UniProt
- A0QXB7
- Ligands
- FE, FE2, MG, CL
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps | protein | 161 | 70% helix, 2% strand | A0QXB7 |
| B | Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps | protein | 160 | 73% helix, 3% strand | A0QXB7 |
| C | Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps | protein | 159 | 73% helix, 3% strand | A0QXB7 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- FE2 · Fe (II) ion · metal · 4 copies · chains A, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.75 | 0.99 | 16 | empty |
| 2 | 72 | 0.74 | 0.98 | 18 | empty |
| 3 | 113 | 0.43 | 0.77 | 23 | empty |
| 4 | 53 | 0.32 | 0.77 | 12 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1429 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1408 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1062 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 558 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 54 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5WW8 · Crystal structure of the second DNA-Binding protein under starvation from Mycobacterium… · 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 A0QXB7
- Elsewhere: RCSB PDB 5WW8 · PDBe 5WW8 · UniProt A0QXB7
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