MolNFT v1 · #111516 · protein
Hmdii from methanocaldococcus jannaschii with bound methylene- tetrahydromethanopterin
4YT5 · H(2)-forming methylenetetrahydromethanopterin…: “Hmdii from methanocaldococcus jannaschii with bound methylene- tetrahydromethanopterin”. X-ray diffraction, 1 ligand (H4M), 7 pockets (best druggability 0.76). MolNFT v1 #111516 on…
- PDB
- 4YT5
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
- UniProt
- Q58734
- Ligands
- H4M
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338 | protein | 344 | 56% helix, 11% strand | Q58734 |
Ligands and binding sites
- H4M · 5,10-dimethylene tetrahydromethanopterin · ligand · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.76 | 0.86 | 46 | H4M |
| 2 | 393 | 0.74 | 0.84 | 54 | H4M |
| 3 | 86 | 0.51 | 0.83 | 23 | empty |
| 4 | 116 | 0.49 | 0.80 | 17 | empty |
| 5 | 74 | 0.49 | 0.83 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 6157 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4YT5 · HmdII from Methanocaldococcus jannaschii with bound methylene-tetrahydromethanopterin · 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 0.98
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 4YT5 · PDBe 4YT5 · UniProt Q58734
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