Research workbench
Crystal structure of log (RV1205) from mycobacterium tuberculosis
Analyse Crystal structure of log (RV1205) from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W2I
- Type
- protein
- Length
- 714 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytokinin riboside 5'-monophosphate phosphoribohydrolase
- EC
- 3.2.2.-
- UniProt
- A0A045J166
- Ligands
- MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 183 | 46% helix, 18% strand | A0A045J166 |
| B, C, D | Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.-) | protein | 177 | 47% helix, 19% strand | A0A045J166 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.72 | 0.90 | 31 | empty |
| 2 | 540 | 0.69 | 0.79 | 60 | empty |
| 3 | 460 | 0.67 | 0.79 | 50 | EDO |
| 4 | 89 | 0.41 | 0.78 | 24 | empty |
| 5 | 66 | 0.40 | 0.80 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1711 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 354 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 135 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 35 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7W2I · Crystal structure of LOG (Rv1205) from Mycobacterium tuberculosis · 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 A0A045J166
- Elsewhere: RCSB PDB 7W2I · PDBe 7W2I · UniProt A0A045J166
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