MolNFT v1 · #114935 · protein
Conformational alternate of sisomicin in complex with APH(2")-iva
5C4L · APH(2'')-id: “Conformational alternate of sisomicin in complex with APH(2")-iva”. X-ray diffraction, 2 ligands (4XR, SIS), 7 pockets (best druggability 0.77). MolNFT v1 #114935 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5C4L
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- APH(2'')-id
- UniProt
- O68183
- Ligands
- 4XR, SIS
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | APH(2'')-id | protein | 297 | 47% helix, 15% strand | O68183 |
Ligands and binding sites
- 4XR · (2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-ol · ligand · chains A
- 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.77 | 0.79 | 76 | 4XR |
| 2 | 1026 | 0.75 | 0.78 | 81 | SIS |
| 3 | 860 | 0.70 | 0.75 | 60 | empty |
| 4 | 65 | 0.33 | 0.76 | 15 | empty |
| 5 | 61 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 102 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5C4L · Conformational alternate of sisomicin in complex with APH(2")-IVa · 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 O68183
- Elsewhere: RCSB PDB 5C4L · PDBe 5C4L · UniProt O68183
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