Research workbench
Binding of 5'-GTP to molybdenum cofactor biosynthesis protein moac from thermus theromophilus HB8
Analyse Binding of 5'-GTP to molybdenum cofactor biosynthesis protein moac from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JQM
- Type
- protein
- Length
- 1,322 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molybdenum cofactor biosynthesis protein C
- UniProt
- Q5SHE1
- Ligands
- GTP
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Molybdenum cofactor biosynthesis protein C | protein | 147 | 32% helix, 33% strand | Q5SHE1 |
| B, F, G, H | Molybdenum cofactor biosynthesis protein C | protein | 146 | 33% helix, 33% strand | Q5SHE1 |
| E | Molybdenum cofactor biosynthesis protein C | protein | 149 | 33% helix, 33% strand | Q5SHE1 |
| I | Molybdenum cofactor biosynthesis protein C | protein | 148 | 30% helix, 33% strand | Q5SHE1 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 9 copies · chains A, B, E, C, G, D, F, H, I
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, E, B, C, D, H, F, G, I
- FLC · Citrate anion · additive · 9 copies · chains A, B, E, C, G, D, F, H, I
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, E, C, F, G, I, H
- GOL · Glycerol · additive · 5 copies · chains A, C, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.89 | 0.91 | 126 | PEG, EDO |
| 2 | 239 | 0.63 | 0.82 | 31 | GTP, FLC |
| 3 | 174 | 0.63 | 0.85 | 27 | FLC, GTP |
| 4 | 412 | 0.60 | 0.76 | 42 | EDO |
| 5 | 223 | 0.59 | 0.80 | 29 | GTP, FLC |
Interfaces
23 interfaces between chains.
- D–F · 1834 Ų buried · 14 hydrogen bonds · protein-protein
- C–G · 1828 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 1812 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 1810 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 861 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3JQM · Binding of 5'-GTP to molybdenum cofactor biosynthesis protein MoaC from Thermus… · the same entry in another collection · chain D against D, 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 Q5SHE1
- Elsewhere: RCSB PDB 3JQM · PDBe 3JQM · UniProt Q5SHE1
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