Research workbench
Structure in P1 form of the pbp agtb in complex with agropinic acid from A.TUMEFACIEN R10
Analyse Structure in P1 form of the pbp agtb in complex with agropinic acid from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HM2
- Type
- protein
- Length
- 1,573 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agropine permease
- UniProt
- W8FRA6
- Ligands
- G9Z, NA
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agropine permease | protein | 316 | 46% helix, 20% strand | W8FRA6 |
| B | Agropine permease | protein | 317 | 45% helix, 20% strand | W8FRA6 |
| C, D | Agropine permease | protein | 314 | 46% helix, 20% strand | W8FRA6 |
| E | Agropine permease | protein | 312 | 46% helix, 20% strand | W8FRA6 |
Ligands and binding sites
- G9Z · agropinic acid · ligand · 5 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.79 | 0.81 | 80 | G9Z |
| 2 | 409 | 0.74 | 0.84 | 46 | empty |
| 3 | 1098 | 0.74 | 0.77 | 71 | EDO |
| 4 | 684 | 0.73 | 0.80 | 67 | empty |
| 5 | 288 | 0.71 | 0.85 | 40 | G9Z, NA |
Interfaces
7 interfaces between chains.
- B–D · 571 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 544 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 411 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 393 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 214 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6HM2 · Structure in P1 form of the PBP AgtB in complex with agropinic acid from A.tumefacien R10 · the same entry in another collection · chain C against C, 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 6HM2 · PDBe 6HM2 · UniProt W8FRA6
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