Research workbench
Structure of the METHANOFURAN/METHANOPTERIN biosynthetic enzyme MJ1099 from methanocaldococcus jannaschii with prpp
Analyse Structure of the METHANOFURAN/METHANOPTERIN biosynthetic enzyme MJ1099 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RC1
- Type
- protein
- Length
- 2,136 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0264 protein MJ1099
- UniProt
- Q58499
- Ligands
- PO4
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0264 protein MJ1099 | protein | 241 | 44% helix, 19% strand | Q58499 |
| B, D | UPF0264 protein MJ1099 | protein | 242 | 45% helix, 19% strand | Q58499 |
| C, E, G, I | UPF0264 protein MJ1099 | protein | 236 | 46% helix, 19% strand | Q58499 |
| F | UPF0264 protein MJ1099 | protein | 238 | 45% helix, 19% strand | Q58499 |
| H | UPF0264 protein MJ1099 | protein | 229 | 47% helix, 19% strand | Q58499 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains B, C, D, E, F, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.77 | 0.82 | 76 | empty |
| 2 | 481 | 0.67 | 0.79 | 56 | empty |
| 3 | 118 | 0.58 | 0.85 | 40 | PO4 |
| 4 | 101 | 0.58 | 0.86 | 34 | empty |
| 5 | 77 | 0.57 | 0.88 | 34 | empty |
Interfaces
13 interfaces between chains.
- A–D · 1130 Ų buried · 13 hydrogen bonds · protein-protein
- B–G · 1117 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 1110 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1109 Ų buried · 12 hydrogen bonds · protein-protein
- G–I · 820 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4RC1 · Structure of the methanofuran/methanopterin biosynthetic enzyme MJ1099 from… · the same entry in another collection · chain I against I, TM-score 1.00
- Q58499 · AlphaFold monomer V2.0 prediction for (5-formylfuran-3-YL)METHYL phosphate synthase… · a predicted model of the same protein · chain C 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 Q58499
- Elsewhere: RCSB PDB 4RC1 · PDBe 4RC1 · UniProt Q58499
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