Research workbench
Crystal structure of protein of unknown function from mine drainage metagenome leptospirillum rubarum
Analyse Crystal structure of protein of unknown function from mine drainage metagenome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NA2
- Type
- protein
- Length
- 537 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A3EUC6
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 138 | 25% helix, 41% strand | A3EUC6 |
| B | Uncharacterized protein | protein | 131 | 27% helix, 40% strand | A3EUC6 |
| C | Uncharacterized protein | protein | 131 | 27% helix, 44% strand | A3EUC6 |
| D | Uncharacterized protein | protein | 137 | 26% helix, 40% strand | A3EUC6 |
Ligands and binding sites
- ACY · Acetic acid · additive · 2 copies · chains A, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.77 | 0.79 | 112 | empty |
| 2 | 210 | 0.60 | 0.81 | 35 | empty |
| 3 | 183 | 0.54 | 0.79 | 29 | empty |
| 4 | 58 | 0.28 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 541 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 459 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 416 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 347 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 330 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3NA2 · Crystal Structure of Protein of Unknown Function from Mine Drainage Metagenome… · 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 A3EUC6
- Elsewhere: RCSB PDB 3NA2 · PDBe 3NA2 · UniProt A3EUC6
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