Research workbench
The crystal structure of terb co-crystallized with polyporic acid
Analyse The crystal structure of terb co-crystallized with polyporic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ND7
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terb oxidoreductase
- Ligands
- NDP, KJG
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Terb oxidoreductase | protein | 313 | 38% helix, 19% strand | — |
| B | Terb oxidoreductase | protein | 307 | 38% helix, 21% strand | — |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- KJG · 2~3~,2~6~-dihydroxy[1~1~,2~1~:2~4~,3~1~-terphenyl]-2~2~,2~5~-dione · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- IPA · Isopropyl alcohol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.73 | 0.83 | 48 | NDP, KJG |
| 2 | 486 | 0.72 | 0.81 | 49 | NDP, KJG |
| 3 | 89 | 0.44 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1325 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6ND7 · The crystal structure of TerB co-crystallized with polyporic acid · 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 6ND7 · PDBe 6ND7
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