Research workbench
Molybdenum storage protein - P212121, ADP, molybdate
Analyse Molybdenum storage protein - P212121, ADP, molybdate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RKE
- Type
- protein
- Length
- 3,238 residues
- Chains
- 12
- 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
- 8M0, ADP, ATP, LJB, M10, LHW, MG, MOO, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, H | Molybdenum storage protein subunit beta | protein | 268 | 43% helix, 15% strand | P84253 |
| A, E, G, I, K | Molybdenum storage protein subunit alpha | protein | 272 | 42% helix, 15% strand | P84308 |
| C | Molybdenum storage protein subunit alpha | protein | 271 | 43% helix, 15% strand | P84308 |
| F | Molybdenum storage protein subunit beta | protein | 269 | 42% helix, 15% strand | P84253 |
| J, L | Molybdenum storage protein subunit beta | protein | 267 | 42% helix, 15% strand | P84253 |
Ligands and binding sites
- 8M0 · bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI) · ligand · 12 copies · chains B, A, D, C, F, E, H, G, J, I, L, K
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains B, A, D, C, F, E, H, G, J, I, L, K
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains B, A, D, C, F, E, H, G, J, I, L, K
- LJB · MO(8)-O(26) Cluster · ligand · 2 copies · chains B, D, F, H, J, L
- M10 · (mu3-oxo)-tris(mu2-oxo)-nonakisoxo-trimolybdenum (VI) · ligand · 2 copies · chains A, C, E, G, I, K
- LHW · MO(10)-O(35) Cluster · ligand · 2 copies · chains A, C, E, G, I, K
- MG · Magnesium ion · metal · 12 copies · chains B, A, D, C, F, E, H, G, J, I, L, K
- MOO · Molybdate ion · ion · 6 copies · chains B, A, D, C, F, E, H, G, J, I, L, K
- PO4 · Phosphate ion · ion · 6 copies · chains B, D, F, H, J, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.79 | 0.81 | 160 | 8M0 |
| 2 | 198 | 0.79 | 0.94 | 39 | ADP, MG, MOO, PO4 |
| 3 | 169 | 0.78 | 0.95 | 36 | ADP, MG, MOO, PO4 |
| 4 | 199 | 0.78 | 0.93 | 37 | ADP, MG, MOO, PO4 |
| 5 | 195 | 0.78 | 0.93 | 39 | ADP, MG, MOO, PO4 |
Interfaces
36 interfaces between chains.
- L–K · 3487 Ų buried · 45 hydrogen bonds · protein-protein
- F–E · 3479 Ų buried · 47 hydrogen bonds · protein-protein
- D–C · 3443 Ų buried · 47 hydrogen bonds · protein-protein
- H–G · 3434 Ų buried · 42 hydrogen bonds · protein-protein
- J–I · 3428 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 6RKE · Molybdenum storage protein - P212121, ADP, molybdate · the same entry in another collection · chain K against K, 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 P84253
- Every structure of UniProt P84308
- Elsewhere: RCSB PDB 6RKE · PDBe 6RKE · UniProt P84253 · UniProt P84308
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