Research workbench
Reduced hcgd from methanocaldococcus jannaschii with citrate
Analyse Reduced hcgd from methanocaldococcus jannaschii with citrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WSG
- Type
- protein
- Length
- 1,474 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative GTP cyclohydrolase 1 type 2
- Ligands
- FE2
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative GTP cyclohydrolase 1 type 2 | protein | 248 | 39% helix, 23% strand | — |
| B, C, F | Putative GTP cyclohydrolase 1 type 2 | protein | 245 | 39% helix, 23% strand | — |
| D | Putative GTP cyclohydrolase 1 type 2 | protein | 247 | 39% helix, 23% strand | — |
| E | Putative GTP cyclohydrolase 1 type 2 | protein | 244 | 39% helix, 22% strand | — |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 6 copies · chains A, B, D, C, E, F
- CIT · Citric acid · additive · 6 copies · chains A, F, B, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.77 | 0.79 | 108 | CIT |
| 2 | 1076 | 0.77 | 0.79 | 106 | CIT |
| 3 | 1116 | 0.77 | 0.79 | 105 | CIT |
| 4 | 379 | 0.59 | 0.76 | 48 | empty |
| 5 | 341 | 0.59 | 0.76 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1295 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 1289 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1287 Ų buried · 35 hydrogen bonds · protein-protein
- A–F · 749 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 740 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3WSG · Reduced HcgD from Methanocaldococcus jannaschii with citrate · 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 3WSG · PDBe 3WSG
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