Research workbench
Structure of the pbp agaa in complex with agropinic acid from A.TUMEFACIEN R10
Analyse Structure of the pbp agaa in complex with agropinic acid from A.TUMEFACIEN R10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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