MolNFT v1 · #138648 · protein
Crystal structure of mnda pyd with mbp tag
5WPZ · Mbp-hmnda-pyd: “Crystal structure of mnda pyd with mbp tag”. X-ray diffraction, 1 ligand (GLC), 20 pockets (best druggability 0.81). MolNFT v1 #138648 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WPZ
- Type
- protein
- Length
- 2,764 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mbp-hmnda-pyd
- Ligands
- GLC
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mbp-hmnda-pyd | protein | 460 | 51% helix, 17% strand | — |
| B | Mbp-hmnda-pyd | protein | 462 | 51% helix, 16% strand | — |
| C | Mbp-hmnda-pyd | protein | 461 | 54% helix, 17% strand | — |
| D, F | Mbp-hmnda-pyd | protein | 459 | 51% helix, 17% strand | — |
| E | Mbp-hmnda-pyd | protein | 463 | 52% helix, 17% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.81 | 0.82 | 84 | empty |
| 2 | 944 | 0.80 | 0.82 | 97 | empty |
| 3 | 1066 | 0.79 | 0.81 | 79 | empty |
| 4 | 979 | 0.79 | 0.81 | 92 | empty |
| 5 | 1187 | 0.75 | 0.78 | 107 | empty |
Interfaces
7 interfaces between chains.
- A–D · 844 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 800 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 667 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 595 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 561 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5WPZ · Crystal structure of MNDA 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 5WPZ · PDBe 5WPZ
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