Research workbench
Binary (sisomicin) structure of aac-iiib
Analyse Binary (sisomicin) structure of aac-iiib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MB4
- Type
- protein
- Length
- 1,060 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AAC(3)-iiib protein
- UniProt
- Q51405
- Ligands
- SIS
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | AAC(3)-iiib protein | protein | 265 | 34% helix, 22% strand | Q51405 |
Ligands and binding sites
- SIS · (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside · ligand · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.81 | 0.87 | 94 | empty |
| 2 | 302 | 0.66 | 0.81 | 47 | empty |
| 3 | 360 | 0.63 | 0.79 | 46 | empty |
| 4 | 261 | 0.59 | 0.79 | 35 | empty |
| 5 | 237 | 0.58 | 0.79 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1188 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 467 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 302 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 217 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 117 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MB4 · Binary (sisomicin) 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 6MB4 · PDBe 6MB4 · UniProt Q51405
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