MolNFT v1 · #181327 · protein
C-terminal domain of ribd from brucella abortus (5-amino-6- ribosylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate reductase)
7LRH · Riboflavin biosynthesis protein ribd: “C-terminal domain of ribd from brucella abortus (5-amino-6- ribosylamino-2,4(1H,3H)-pyrimidinedione…”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.73). MolNFT v1 #181327…
- PDB
- 7LRH
- Type
- protein
- Length
- 850 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin biosynthesis protein ribd
- EC
- 3.5.4.26, 1.1.1.193
- UniProt
- A0A4V1RP59
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin biosynthesis protein ribd (EC 3.5.4.26, 1.1.1.193) | protein | 212 | 31% helix, 26% strand | A0A4V1RP59 |
| B | Riboflavin biosynthesis protein ribd (EC 3.5.4.26, 1.1.1.193) | protein | 213 | 30% helix, 28% strand | A0A4V1RP59 |
| C | Riboflavin biosynthesis protein ribd (EC 3.5.4.26, 1.1.1.193) | protein | 212 | 30% helix, 27% strand | A0A4V1RP59 |
| D | Riboflavin biosynthesis protein ribd (EC 3.5.4.26, 1.1.1.193) | protein | 213 | 30% helix, 25% strand | A0A4V1RP59 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.73 | 0.95 | 19 | empty |
| 2 | 684 | 0.70 | 0.77 | 47 | empty |
| 3 | 326 | 0.67 | 0.81 | 36 | empty |
| 4 | 315 | 0.61 | 0.79 | 44 | SO4 |
| 5 | 208 | 0.59 | 0.81 | 24 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 991 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 879 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 487 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7LRH · C-terminal domain of RibD from Brucella abortus… · 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 A0A4V1RP59
- Elsewhere: RCSB PDB 7LRH · PDBe 7LRH · UniProt A0A4V1RP59
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