Research workbench
Wzc-K540M mgadp C1
Analyse Wzc-K540M mgadp C1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NII
- Type
- protein
- Length
- 4,772 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative transmembrane protein wzc
- UniProt
- Q9X4B9
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Putative transmembrane protein wzc | protein | 663 | 50% helix, 19% strand | Q9X4B9 |
| B, G | Putative transmembrane protein wzc | protein | 564 | 43% helix, 22% strand | Q9X4B9 |
| C, H | Putative transmembrane protein wzc | protein | 565 | 43% helix, 23% strand | Q9X4B9 |
| E | Putative transmembrane protein wzc | protein | 525 | 39% helix, 24% strand | Q9X4B9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, H, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.81 | 0.86 | 68 | empty |
| 2 | 757 | 0.80 | 0.84 | 77 | empty |
| 3 | 597 | 0.80 | 0.85 | 68 | empty |
| 4 | 152 | 0.74 | 0.92 | 34 | empty |
| 5 | 569 | 0.72 | 0.80 | 47 | empty |
Interfaces
8 interfaces between chains.
- B–C · 2534 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2518 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2171 Ų buried · 29 hydrogen bonds · protein-protein
- A–H · 2142 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2126 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7NII · Wzc-K540M MgADP C1 · 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
- Every structure of UniProt Q9X4B9
- Elsewhere: RCSB PDB 7NII · PDBe 7NII · UniProt Q9X4B9
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