MolNFT v1 · #151371 · protein
Structure of the pbp agaa in complex with agropinic acid from A.TUMEFACIEN R10
6HLX: “Structure of the pbp agaa in complex with agropinic acid from A.TUMEFACIEN R10”. X-ray diffraction, 3 ligands (G9Z, ZN, SO4), 6 pockets (best druggability 0.74). MolNFT v1 #151371 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HLX
- Type
- protein
- Length
- 491 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agaa
- UniProt
- O50260
- Ligands
- G9Z, ZN, SO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agaa | protein | 491 | 33% helix, 21% strand | O50260 |
Ligands and binding sites
- G9Z · agropinic acid · ligand · chains A
- ZN · Zinc ion · metal · 6 copies · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 14 copies · chains A
- ACT · Acetate ion · additive · 7 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.74 | 0.95 | 33 | G9Z |
| 2 | 75 | 0.58 | 0.88 | 21 | EDO |
| 3 | 118 | 0.55 | 0.83 | 23 | EDO |
| 4 | 70 | 0.47 | 0.84 | 19 | ACT |
| 5 | 73 | 0.47 | 0.82 | 18 | GOL |
Compared structures
- 6HLX · Structure of the PBP AgaA in complex with agropinic acid from A.tumefacien R10 · 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 O50260
- Elsewhere: RCSB PDB 6HLX · PDBe 6HLX · UniProt O50260
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.