Research workbench
Crystal structure of a putative DNA binding protein (BT_1116) from bacteroides thetaiotaomicron vpi-5482 at 1.50 a resolution
Analyse Crystal structure of a putative DNA binding protein (BT_1116) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HTN
- Type
- protein
- Length
- 425 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative DNA binding protein
- UniProt
- Q8A8Q1
- Ligands
- NI, FE, SO4
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative DNA binding protein | protein | 143 | 8% helix, 64% strand | Q8A8Q1 |
| B | Putative DNA binding protein | protein | 139 | 8% helix, 63% strand | Q8A8Q1 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, C, B
- FE · Fe (III) ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · 5 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.83 | 0.95 | 52 | empty |
| 2 | 195 | 0.57 | 0.80 | 31 | 1PE |
| 3 | 152 | 0.56 | 0.81 | 29 | NI, 1PE |
| 4 | 146 | 0.54 | 0.81 | 27 | FE |
Interfaces
3 interfaces between chains.
- A–B · 1314 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1295 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1292 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3HTN · Crystal structure of a putative dna binding protein (bt_1116) from bacteroides… · 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 Q8A8Q1
- Elsewhere: RCSB PDB 3HTN · PDBe 3HTN · UniProt Q8A8Q1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.