Research workbench
Crystal structure of a prokaryotic domain of unknown function (DUF849) with a tim barrel fold (BXE_C0966) from burkholderia xenovorans LB400 at 1.75 a resolution
Analyse Crystal structure of a prokaryotic domain of unknown function (DUF849) with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E49
- Type
- protein
- Length
- 1,228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein DUF849 with a tim barrel fold
- UniProt
- Q13GE9
- Ligands
- ETX, ZN
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Uncharacterized protein DUF849 with a tim barrel fold | protein | 307 | 43% helix, 18% strand | Q13GE9 |
Ligands and binding sites
- ETX · 2-ethoxyethanol · ligand · 7 copies · chains A, B, C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- IMD · Imidazole · additive · 5 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.74 | 0.79 | 84 | ETX, IMD |
| 2 | 669 | 0.73 | 0.80 | 79 | IMD |
| 3 | 518 | 0.73 | 0.81 | 59 | IMD |
| 4 | 457 | 0.71 | 0.81 | 56 | empty |
| 5 | 262 | 0.63 | 0.81 | 34 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1467 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1464 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 872 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 850 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3E49 · Crystal structure of a prokaryotic domain of unknown function (duf849) with a tim barrel… · 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 Q13GE9
- Elsewhere: RCSB PDB 3E49 · PDBe 3E49 · UniProt Q13GE9
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