MolNFT v1 · #98661 · protein
Crystal structure of a DUF487 family protein (DESPIG_00776) from desulfovibrio piger atcc 29098 at 2.49 a resolution
4LG3 · Uncharacterized protein: “Crystal structure of a DUF487 family protein (DESPIG_00776) from desulfovibrio piger atcc 29098 at 2.49 a…”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.78). MolNFT v1 #98661 on…
- PDB
- 4LG3
- Type
- protein
- Length
- 539 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- B6WRT5
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein | protein | 179 | 31% helix, 28% strand | B6WRT5 |
| C | Uncharacterized protein | protein | 181 | 30% helix, 31% strand | B6WRT5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, C, B
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 | 605 | 0.78 | 0.84 | 82 | EDO |
| 2 | 316 | 0.70 | 0.83 | 40 | EDO |
| 3 | 130 | 0.56 | 0.82 | 21 | EDO |
| 4 | 54 | 0.28 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 913 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 865 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4LG3 · Crystal structure of a DUF487 family protein (DESPIG_00776) from Desulfovibrio piger ATCC… · 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 B6WRT5
- Elsewhere: RCSB PDB 4LG3 · PDBe 4LG3 · UniProt B6WRT5
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