MolNFT v1 · #128904 · protein
Hcgc from methanococcus maripaludis cocrystallized with SAM and pyridinol
5O4H: “Hcgc from methanococcus maripaludis cocrystallized with SAM and pyridinol”. X-ray diffraction, 3 ligands (SAH, NA, SO4), 16 pockets (best druggability 0.85). MolNFT v1 #128904 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5O4H
- Type
- protein
- Length
- 1,039 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hcgc
- UniProt
- Q6LX54
- Ligands
- SAH, NA, SO4
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hcgc | protein | 260 | 40% helix, 25% strand | Q6LX54 |
| B | Hcgc | protein | 259 | 39% helix, 25% strand | Q6LX54 |
| C | Hcgc | protein | 262 | 39% helix, 25% strand | Q6LX54 |
| D | Hcgc | protein | 258 | 40% helix, 25% strand | Q6LX54 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains D
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.85 | 0.86 | 86 | empty |
| 2 | 287 | 0.81 | 0.92 | 41 | SAH |
| 3 | 273 | 0.81 | 0.92 | 41 | SAH |
| 4 | 417 | 0.79 | 0.88 | 42 | SAH |
| 5 | 570 | 0.75 | 0.82 | 54 | SO4, ACT |
Interfaces
6 interfaces between chains.
- C–D · 1808 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1806 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 890 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 782 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 315 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5O4H · HcgC from Methanococcus maripaludis cocrystallized with SAM and pyridinol · 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 Q6LX54
- Elsewhere: RCSB PDB 5O4H · PDBe 5O4H · UniProt Q6LX54
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