Research workbench
Apo hcgc from methanococcus maripaludis soaked with sah and pyridinol
Analyse Apo hcgc from methanococcus maripaludis soaked with sah and pyridinol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O4N
- Type
- protein
- Length
- 1,045 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hcgc
- UniProt
- Q6LX54
- Ligands
- SAH, 9KH
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hcgc | protein | 264 | 38% helix, 25% strand | Q6LX54 |
| B | Hcgc | protein | 260 | 38% helix, 25% strand | Q6LX54 |
| C | Hcgc | protein | 260 | 38% helix, 26% strand | Q6LX54 |
| D | Hcgc | protein | 261 | 38% helix, 26% strand | Q6LX54 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- 9KH · 6-carboxy methyl-4-hydroxy-2-pyridinol · ligand · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains B, D, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.85 | 0.86 | 81 | empty |
| 2 | 274 | 0.82 | 0.93 | 41 | SAH, 9KH |
| 3 | 276 | 0.81 | 0.92 | 40 | SAH, 9KH |
| 4 | 273 | 0.81 | 0.92 | 41 | SAH, 9KH |
| 5 | 286 | 0.81 | 0.92 | 41 | SAH, 9KH |
Interfaces
6 interfaces between chains.
- A–B · 1955 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1950 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 752 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 277 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5O4N · Apo HcgC from Methanococcus maripaludis soaked with SAH 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 5O4N · PDBe 5O4N · UniProt Q6LX54
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