MolNFT v1 · #68780 · protein
Crystal structure of molybdenum cofactor biosynthesis protein mog from shewanella oneidensis
3K6A: “Crystal structure of molybdenum cofactor biosynthesis protein mog from shewanella oneidensis”. X-ray diffraction, 1 ligand (NA), 10 pockets (best druggability 0.72). MolNFT v1 #68780 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3K6A
- Type
- protein
- Length
- 1,034 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molybdenum cofactor biosynthesis protein mog
- UniProt
- Q8EKM7
- Ligands
- NA
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Molybdenum cofactor biosynthesis protein mog | protein | 176 | 41% helix, 21% strand | Q8EKM7 |
| B, D | Molybdenum cofactor biosynthesis protein mog | protein | 172 | 45% helix, 20% strand | Q8EKM7 |
| C | Molybdenum cofactor biosynthesis protein mog | protein | 173 | 45% helix, 21% strand | Q8EKM7 |
| E | Molybdenum cofactor biosynthesis protein mog | protein | 171 | 45% helix, 20% strand | Q8EKM7 |
| F | Molybdenum cofactor biosynthesis protein mog | protein | 170 | 46% helix, 19% strand | Q8EKM7 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.72 | 0.76 | 70 | empty |
| 2 | 554 | 0.70 | 0.80 | 42 | empty |
| 3 | 600 | 0.70 | 0.78 | 41 | empty |
| 4 | 515 | 0.67 | 0.78 | 47 | empty |
| 5 | 447 | 0.64 | 0.77 | 48 | empty |
Interfaces
8 interfaces between chains.
- D–F · 785 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 740 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 731 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 724 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 719 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 modified (engineered).
Compared structures
- 3K6A · Crystal structure of molybdenum cofactor biosynthesis protein mog from shewanella… · 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 Q8EKM7
- Elsewhere: RCSB PDB 3K6A · PDBe 3K6A · UniProt Q8EKM7
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