Research workbench
Crystal structure of protein MJ0408 from methanococcus jannaschii, pfam DUF372
Analyse Crystal structure of protein MJ0408 from methanococcus jannaschii, pfam DUF372 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OGF
- Type
- protein
- Length
- 486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein MJ0408
- UniProt
- Q57851
- Ligands
- OXG, SO4
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hypothetical protein MJ0408 | protein | 121 | 39% helix, 33% strand | Q57851 |
| B, D | Hypothetical protein MJ0408 | protein | 122 | 40% helix, 34% strand | Q57851 |
Ligands and binding sites
- OXG · 8-oxoguanine · ligand · 4 copies · chains A, C, D, B
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
- GOL · Glycerol · additive · 2 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.74 | 0.83 | 74 | OXG, GOL |
| 2 | 325 | 0.74 | 0.85 | 67 | OXG |
| 3 | 65 | 0.32 | 0.76 | 12 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1512 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1511 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1159 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1154 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 382 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2OGF · Crystal structure of protein MJ0408 from Methanococcus jannaschii, Pfam DUF372 · the same entry in another collection · chain A against A, TM-score 1.00
- Q57851 · AlphaFold monomer V2.0 prediction for dihydroneopterin aldolase (Q57851) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q57851
- Elsewhere: RCSB PDB 2OGF · PDBe 2OGF · UniProt Q57851
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