MolNFT v1 · #138836 · protein
Crystal structure of the second DNA-binding protein under starvation from mycobacterium smegmatis soaked with iron in the ratio of 24 iron atoms per dodecamer
5WW3 · 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 (FE2, FE, MG), 3 pockets…
- PDB
- 5WW3
- Type
- protein
- Length
- 642 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
- FE2, FE, MG, CL
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 2% 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, C | Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps | protein | 160 | 73% helix, 3% strand | A0QXB7 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 6 copies · chains A, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.74 | 0.98 | 19 | empty |
| 2 | 68 | 0.73 | 0.97 | 17 | empty |
| 3 | 79 | 0.36 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1444 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1424 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1077 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 565 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 51 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5WW3 · 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 5WW3 · PDBe 5WW3 · UniProt A0QXB7
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