Research workbench
Molybdenum storage protein - P6422, ADP
Analyse Molybdenum storage protein - P6422, ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RJ4
- Type
- protein
- Length
- 1,550 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molybdenum storage protein subunit beta; Molybdenum storage protein subunit alpha
- UniProt
- P84253, P84308
- Ligands
- ADP, ATP, MG, NA, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Molybdenum storage protein subunit beta | protein | 269 | 43% helix, 16% strand | P84253 |
| A, C | Molybdenum storage protein subunit alpha | protein | 244 | 43% helix, 16% strand | P84308 |
| D, F | Molybdenum storage protein subunit beta | protein | 267 | 43% helix, 16% strand | P84253 |
| E | Molybdenum storage protein subunit alpha | protein | 259 | 42% helix, 15% strand | P84308 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, D, F
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains B, A, D, C, F, E
- MG · Magnesium ion · metal · 4 copies · chains A, D, C, E
- NA · Sodium ion · metal · chains B, D
- PO4 · Phosphate ion · ion · 6 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.78 | 0.98 | 25 | empty |
| 2 | 249 | 0.78 | 0.91 | 38 | ATP, MG |
| 3 | 254 | 0.78 | 0.91 | 38 | ATP, MG |
| 4 | 268 | 0.76 | 0.89 | 39 | ATP, MG |
| 5 | 85 | 0.76 | 0.98 | 20 | empty |
Interfaces
12 interfaces between chains.
- F–E · 2356 Ų buried · 27 hydrogen bonds · protein-protein
- D–C · 2327 Ų buried · 24 hydrogen bonds · protein-protein
- B–A · 2319 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1087 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 1081 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6RJ4 · Molybdenum storage protein - P6422, ADP · the same entry in another collection · chain E against E, TM-score 1.00
- P84308 · AlphaFold monomer V2.0 prediction for molybdenum storage protein subunit alpha (P84308) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P84253 · AlphaFold monomer V2.0 prediction for molybdenum storage protein subunit beta (P84253) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P84253
- Every structure of UniProt P84308
- Elsewhere: RCSB PDB 6RJ4 · PDBe 6RJ4 · UniProt P84253 · UniProt P84308
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