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Structure in C2 form of the pbp agtb from A.TUMEFACIEN R10 in complex with agropinic acid
Analyse Structure in C2 form of the pbp agtb from A.TUMEFACIEN R10 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HLZ
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agropine permease
- UniProt
- W8FRA6
- Ligands
- P4G, G9Z
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agropine permease | protein | 316 | 44% helix, 19% strand | W8FRA6 |
| B | Agropine permease | protein | 316 | 46% helix, 19% strand | W8FRA6 |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 6 copies · chains B
- G9Z · agropinic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 44 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 13 copies · chains A, B
- P6G · Hexaethylene glycol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.74 | 0.77 | 72 | EDO, PEG |
| 2 | 309 | 0.71 | 0.84 | 37 | G9Z |
| 3 | 280 | 0.70 | 0.84 | 40 | EDO, G9Z |
| 4 | 104 | 0.36 | 0.74 | 27 | empty |
| 5 | 50 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 393 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6HLZ · Structure in C2 form of the PBP AgtB from A.tumefacien R10 in complex with agropinic acid · the same entry in another collection · chain B against B, 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 W8FRA6
- Elsewhere: RCSB PDB 6HLZ · PDBe 6HLZ · UniProt W8FRA6
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