MolNFT v1 · #111515 · protein
Iron guanylylpyridinol (fegp) cofactor-reconstituted hmdii from methanocaldococcus jannaschii
4YT4 · H(2)-forming methylenetetrahydromethanopterin…: “Iron guanylylpyridinol (fegp) cofactor-reconstituted hmdii from methanocaldococcus jannaschii”. X-ray diffraction, 1 ligand (FE9), 3 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 4YT4
- Type
- protein
- Length
- 345 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
- UniProt
- Q58734
- Ligands
- FE9
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338 | protein | 345 | 56% helix, 11% strand | Q58734 |
Ligands and binding sites
- FE9 · iron-guanylyl pyridinol cofactor · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.68 | 0.77 | 37 | empty |
| 2 | 509 | 0.61 | 0.74 | 45 | empty |
| 3 | 233 | 0.52 | 0.76 | 33 | FE9 |
Compared structures
- 4YT4 · Iron guanylylpyridinol (FeGP) cofactor-reconstituted HmdII from Methanocaldococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58734 · AlphaFold monomer V2.0 prediction for H(2)-forming methylenetetrahydromethanopterin… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q58734
- Elsewhere: RCSB PDB 4YT4 · PDBe 4YT4 · UniProt Q58734
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