MolNFT v1 · #48753 · protein
Crystal structure of a rmlc-like cupin protein (DDE_2303) from desulfovibrio desulfuricans subsp. at 1.94 a resolution
2Q30 · Uncharacterized protein: “Crystal structure of a rmlc-like cupin protein (DDE_2303) from desulfovibrio desulfuricans subsp. at 1.94 a…”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.78). MolNFT v1 #48753 on…
- PDB
- 2Q30
- Type
- protein
- Length
- 838 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q30YZ6
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Uncharacterized protein | protein | 106 | 3% helix, 55% strand | Q30YZ6 |
| B, C | Uncharacterized protein | protein | 105 | 3% helix, 57% strand | Q30YZ6 |
| E, F, G, H | Uncharacterized protein | protein | 104 | 3% helix, 55% strand | Q30YZ6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.78 | 0.82 | 57 | EDO |
| 2 | 503 | 0.77 | 0.84 | 48 | EDO |
| 3 | 79 | 0.45 | 0.80 | 16 | empty |
| 4 | 81 | 0.44 | 0.79 | 16 | EDO |
| 5 | 188 | 0.44 | 0.74 | 25 | EDO |
Interfaces
8 interfaces between chains.
- C–D · 1591 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1518 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1330 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1329 Ų buried · 23 hydrogen bonds · protein-protein
- D–H · 656 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 2Q30 · Crystal structure of a rmlc-like cupin protein (dde_2303) from desulfovibrio… · 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 Q30YZ6
- Elsewhere: RCSB PDB 2Q30 · PDBe 2Q30 · UniProt Q30YZ6
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