MolNFT v1 · #183879 · protein
Crystal structure of a 2`-deoxyribosyltransferase from the psychrophilic bacterium desulfotalea psychrophila.
7O62 · Chains: A,B,C,D: “Crystal structure of a 2`-deoxyribosyltransferase from the psychrophilic bacterium desulfotalea psychrophila.”. X-ray diffraction, 6 pockets (best druggability 0.79). MolNFT v1 #183879 on GenesisL1: 3D structure…
- PDB
- 7O62
- Type
- protein
- Length
- 531 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chains: A,B,C,D
- UniProt
- Q6AQB0
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chains: A,B,C,D | protein | 135 | 46% helix, 17% strand | Q6AQB0 |
| B | Chains: A,B,C,D | protein | 137 | 45% helix, 17% strand | Q6AQB0 |
| C | Chains: A,B,C,D | protein | 133 | 47% helix, 17% strand | Q6AQB0 |
| D | Chains: A,B,C,D | protein | 126 | 46% helix, 17% strand | Q6AQB0 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.79 | 0.88 | 74 | empty |
| 2 | 363 | 0.76 | 0.86 | 69 | empty |
| 3 | 138 | 0.75 | 0.93 | 32 | GOL |
| 4 | 196 | 0.55 | 0.79 | 29 | GOL |
| 5 | 190 | 0.55 | 0.79 | 27 | GOL |
Interfaces
6 interfaces between chains.
- A–B · 1444 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1361 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 544 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 521 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 324 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7O62 · Crystal structure of a 2`-deoxyribosyltransferase from the psychrophilic bacterium… · 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 Q6AQB0
- Elsewhere: RCSB PDB 7O62 · PDBe 7O62 · UniProt Q6AQB0
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