Research workbench
Edta-treated, oxidized hcgd from methanocaldococcus jannaschii
Analyse Edta-treated, oxidized hcgd from methanocaldococcus jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WSH
- Type
- protein
- Length
- 2,928 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative GTP cyclohydrolase 1 type 2
- Ligands
- FE, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Putative GTP cyclohydrolase 1 type 2 | protein | 244 | 39% helix, 21% strand | — |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, F, D, E, J, G, H, I, K, L
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, F, D, G, E, J, H, I, K, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.77 | 0.79 | 102 | SO4 |
| 2 | 1038 | 0.77 | 0.79 | 97 | SO4 |
| 3 | 1036 | 0.76 | 0.79 | 98 | SO4 |
| 4 | 1050 | 0.76 | 0.78 | 96 | SO4, FE |
| 5 | 1115 | 0.72 | 0.75 | 90 | empty |
Interfaces
20 interfaces between chains.
- C–F · 856 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 772 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 764 Ų buried · 10 hydrogen bonds · protein-protein
- E–J · 753 Ų buried · 10 hydrogen bonds · protein-protein
- D–G · 742 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3WSH · EDTA-treated, oxidized HcgD from Methanocaldococcus jannaschii · 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
- Elsewhere: RCSB PDB 3WSH · PDBe 3WSH
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