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2.7 ångström crystal structure of ABC transporter ATPase from vibrio vulnificus in complex with adenylyl-imidodiphosphate (AMP-pnp)
Analyse 2.7 ångström crystal structure of ABC transporter ATPase from vibrio vulnificus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D6A
- Type
- protein
- Length
- 548 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted ATPase of the ABC class
- UniProt
- Q7MEA1
- Ligands
- ANP, NA
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Predicted ATPase of the ABC class | protein | 548 | 34% helix, 23% strand | Q7MEA1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.61 | 0.76 | 49 | empty |
| 2 | 85 | 0.48 | 0.82 | 25 | empty |
| 3 | 84 | 0.42 | 0.79 | 21 | ANP |
| 4 | 111 | 0.38 | 0.75 | 19 | empty |
| 5 | 71 | 0.30 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5D6A · 2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vibrio vulnificus in… · 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 Q7MEA1
- Elsewhere: RCSB PDB 5D6A · PDBe 5D6A · UniProt Q7MEA1
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