MolNFT v1 · #151373 · protein
Structure in C2 form of the pbp agtb from A.TUMEFACIEN R10 in complex with agropinic acid
6HLZ · Agropine permease: “Structure in C2 form of the pbp agtb from A.TUMEFACIEN R10 in complex with agropinic acid”. X-ray diffraction, 2 ligands (P4G, G9Z), 5 pockets (best druggability 0.74). MolNFT v1 #151373 on GenesisL1: 3D…
- 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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