MolNFT v1 · #138654 · protein
Crystal structure of hmnda-pyd with mbp tag
5WQ6 · Mbp tagged hmnda-pyd: “Crystal structure of hmnda-pyd with mbp tag”. X-ray diffraction, 1 ligand (GLC), 17 pockets (best druggability 0.82). MolNFT v1 #138654 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WQ6
- Type
- protein
- Length
- 1,862 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mbp tagged hmnda-pyd
- Ligands
- GLC
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mbp tagged hmnda-pyd | protein | 467 | 54% helix, 16% strand | — |
| B | Mbp tagged hmnda-pyd | protein | 465 | 53% helix, 17% strand | — |
| C | Mbp tagged hmnda-pyd | protein | 464 | 54% helix, 16% strand | — |
| D | Mbp tagged hmnda-pyd | protein | 466 | 53% helix, 17% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, B
- ACT · Acetate ion · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.82 | 0.83 | 117 | GLC |
| 2 | 974 | 0.81 | 0.82 | 97 | EDO |
| 3 | 1179 | 0.79 | 0.80 | 82 | EDO |
| 4 | 1052 | 0.76 | 0.78 | 94 | GLC, EDO |
| 5 | 772 | 0.74 | 0.79 | 72 | GLC, EDO |
Interfaces
4 interfaces between chains.
- A–B · 820 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 674 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 670 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 652 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5WQ6 · Crystal Structure of hMNDA-PYD with MBP tag · 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 5WQ6 · PDBe 5WQ6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.