MolNFT v1 · #156657 · protein
Ternary (NEOMYCIN/COA) structure of aac-iiib
6MB9 · AAC(3)-iiib protein: “Ternary (NEOMYCIN/COA) structure of aac-iiib”. X-ray diffraction, 2 ligands (COA, NMY), 11 pockets (best druggability 0.85). MolNFT v1 #156657 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MB9
- Type
- protein
- Length
- 1,061 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AAC(3)-iiib protein
- UniProt
- Q51405
- Ligands
- COA, NMY
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | AAC(3)-iiib protein | protein | 265 | 35% helix, 22% strand | Q51405 |
| C | AAC(3)-iiib protein | protein | 266 | 36% helix, 23% strand | Q51405 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, C, B, D
- NMY · Neomycin · ligand · 4 copies · chains A, B, C, D
- 2PE · Nonaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.85 | 0.86 | 99 | 2PE |
| 2 | 544 | 0.78 | 0.85 | 76 | empty |
| 3 | 666 | 0.77 | 0.83 | 79 | empty |
| 4 | 347 | 0.66 | 0.80 | 49 | NMY |
| 5 | 365 | 0.63 | 0.78 | 46 | NMY |
Interfaces
5 interfaces between chains.
- A–C · 1158 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1158 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 530 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 510 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 484 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6MB9 · Ternary (neomycin/CoA) structure of AAC-IIIb · 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 Q51405
- Elsewhere: RCSB PDB 6MB9 · PDBe 6MB9 · UniProt Q51405
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