MolNFT v1 · #99425 · protein
Crystal structure of gated-pore mutant D138H of second DNA-binding protein under starvation from mycobacterium smegmatis
4M34 · Putative starvation-induced DNA protecting PROTEIN/FERRITIN…: “Crystal structure of gated-pore mutant D138H of second DNA-binding protein under starvation from…”. X-ray diffraction, 3 ligands (MG, FE2, CL), 4 pockets (best…
- PDB
- 4M34
- Type
- protein
- Length
- 632 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
- MG, FE2, CL
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps | protein | 160 | 71% helix, 3% strand | A0QXB7 |
| B | Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps | protein | 157 | 74% helix, 3% strand | A0QXB7 |
| C | Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps | protein | 156 | 74% helix, 3% strand | A0QXB7 |
| D | Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps | protein | 159 | 73% helix, 3% strand | A0QXB7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, D
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, D
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 | 0.98 | 17 | empty |
| 2 | 68 | 0.73 | 0.98 | 18 | empty |
| 3 | 65 | 0.34 | 0.76 | 14 | empty |
| 4 | 60 | 0.29 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1445 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1436 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1061 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 565 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 53 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4M34 · Crystal structure of gated-pore mutant D138H of second DNA-Binding protein under… · 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 4M34 · PDBe 4M34 · UniProt A0QXB7
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