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Crystal structure of protein of unknown function (NP_070038.1) from archaeoglobus fulgidus at 1.89 a resolution
Analyse Crystal structure of protein of unknown function (NP_070038.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LOT
- Type
- protein
- Length
- 1,244 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- O29058
- Ligands
- UNL, ZN
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uncharacterized protein | protein | 310 | 45% helix, 19% strand | O29058 |
| B | Uncharacterized protein | protein | 311 | 45% helix, 19% strand | O29058 |
| D | Uncharacterized protein | protein | 313 | 43% helix, 19% strand | O29058 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.80 | 0.81 | 109 | UNL |
| 2 | 949 | 0.76 | 0.78 | 95 | ZN, UNL |
| 3 | 498 | 0.73 | 0.81 | 57 | ZN, UNL |
| 4 | 492 | 0.72 | 0.81 | 51 | UNL |
| 5 | 322 | 0.59 | 0.77 | 43 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1484 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1484 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 791 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 784 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 98 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 modified (engineered).
Compared structures
- 3LOT · Crystal structure of PROTEIN OF UNKNOWN FUNCTION (NP_070038.1) from ARCHAEOGLOBUS… · the same entry in another collection · chain C against C, 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 O29058
- Elsewhere: RCSB PDB 3LOT · PDBe 3LOT · UniProt O29058
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