MolNFT v1 · #148543 · protein
Binary complex of a 7S-cis-cis-nepetalactol cyclase from nepeta mussinii with NAD+
6F9Q: “Binary complex of a 7S-cis-cis-nepetalactol cyclase from nepeta mussinii with NAD+”. X-ray diffraction, 2 ligands (NAD, CL), 13 pockets (best druggability 0.85). MolNFT v1 #148543 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6F9Q
- Type
- protein
- Length
- 1,032 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7S-cis-cis-nepetalactol cyclase
- EC
- 5.4.99.-
- Ligands
- NAD, CL
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 7S-cis-cis-nepetalactol cyclase (EC 5.4.99.-) | protein | 257 | 48% helix, 16% strand | — |
| C | 7S-cis-cis-nepetalactol cyclase (EC 5.4.99.-) | protein | 260 | 48% helix, 15% strand | — |
| D | 7S-cis-cis-nepetalactol cyclase (EC 5.4.99.-) | protein | 258 | 48% helix, 16% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.85 | 0.87 | 104 | empty |
| 2 | 473 | 0.79 | 0.87 | 50 | NAD, CL |
| 3 | 481 | 0.79 | 0.86 | 51 | NAD, CL |
| 4 | 493 | 0.78 | 0.85 | 52 | NAD, CL |
| 5 | 475 | 0.77 | 0.85 | 50 | NAD, CL |
Interfaces
6 interfaces between chains.
- A–D · 1699 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1689 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1459 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1391 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 182 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6F9Q · Binary complex of a 7S-cis-cis-nepetalactol cyclase from Nepeta mussinii with NAD+ · 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 6F9Q · PDBe 6F9Q
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