MolNFT v1 · #34386 · protein
Crystal structure of TT0972 protein form thermus thermophilus with MN2(+) ions
2DEG: “Crystal structure of TT0972 protein form thermus thermophilus with MN2(+) ions”. X-ray diffraction, 2 ligands (MN, NA), 4 pockets (best druggability 0.63). MolNFT v1 #34386 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2DEG
- Type
- protein
- Length
- 404 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TT0972 protein
- Ligands
- MN, NA
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TT0972 protein | protein | 68 | 22% helix, 53% strand | — |
| C, D, E, F | TT0972 protein | protein | 67 | 22% helix, 54% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.63 | 0.79 | 28 | empty |
| 2 | 81 | 0.41 | 0.79 | 12 | GOL |
| 3 | 128 | 0.41 | 0.75 | 23 | GOL |
| 4 | 52 | 0.30 | 0.76 | 15 | empty |
Interfaces
9 interfaces between chains.
- E–F · 628 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 612 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 606 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 604 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 582 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2DEG · Crystal structure of tt0972 protein form Thermus Thermophilus with Mn2(+) ions · 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
- Elsewhere: RCSB PDB 2DEG · PDBe 2DEG
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