Research workbench
Crystal structure of an auxiliary nutrient binding protein (BT_3476) from bacteroides thetaiotaomicron vpi-5482 at 2.23 a resolution
Analyse Crystal structure of an auxiliary nutrient binding protein (BT_3476) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TC9
- Type
- protein
- Length
- 843 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical hydrolase
- UniProt
- Q8A230
- Ligands
- PO4, CL
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical hydrolase | protein | 421 | 5% helix, 51% strand | Q8A230 |
| B | Hypothetical hydrolase | protein | 422 | 4% helix, 51% strand | Q8A230 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.70 | 0.81 | 35 | empty |
| 2 | 464 | 0.70 | 0.80 | 34 | empty |
| 3 | 491 | 0.59 | 0.74 | 43 | EDO |
| 4 | 297 | 0.51 | 0.74 | 42 | EDO |
| 5 | 169 | 0.41 | 0.73 | 25 | EDO |
Interfaces
1 interface between chains.
- A–B · 523 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3TC9 · Crystal structure of an auxiliary nutrient binding protein (BT_3476) 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 Q8A230
- Elsewhere: RCSB PDB 3TC9 · PDBe 3TC9 · UniProt Q8A230
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