Research workbench
Crystal structure of human NBD2 complexed with N6-phenylethyl-ATP (P- ATP)
Analyse Crystal structure of human NBD2 complexed with N6-phenylethyl-ATP (P- ATP) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GD7
- Type
- protein
- Length
- 1,506 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427…
- UniProt
- P13569, P68187
- Ligands
- B44
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and MALTOSE/MALTODEXTRIN import ATP- binding protein malk, residues 219-371 | protein | 378 | 23% helix, 32% strand | P13569, P68187 |
| B | Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and MALTOSE/MALTODEXTRIN import ATP- binding protein malk, residues 219-371 | protein | 377 | 23% helix, 34% strand | P13569, P68187 |
| C | Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and MALTOSE/MALTODEXTRIN import ATP- binding protein malk, residues 219-371 | protein | 376 | 22% helix, 33% strand | P13569, P68187 |
| D | Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and MALTOSE/MALTODEXTRIN import ATP- binding protein malk, residues 219-371 | protein | 375 | 23% helix, 33% strand | P13569, P68187 |
Ligands and binding sites
- B44 · N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.78 | 0.82 | 77 | B44 |
| 2 | 494 | 0.72 | 0.81 | 47 | empty |
| 3 | 542 | 0.69 | 0.79 | 42 | empty |
| 4 | 322 | 0.67 | 0.81 | 38 | empty |
| 5 | 348 | 0.65 | 0.80 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–C · 766 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 696 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 612 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 535 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 430 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3GD7 · Crystal structure of human NBD2 complexed with N6-Phenylethyl-ATP (P-ATP) · the same entry in another collection · chain A against A, TM-score 1.00
- P68187 · AlphaFold monomer V2.0 prediction for MALTOSE/MALTODEXTRIN import ATP-binding protein… · a predicted model of the same protein · chain A against A, TM-score 0.81
- P13569 · AlphaFold monomer V2.0 prediction for cystic fibrosis transmembrane conductance regulator… · a predicted model of the same protein · chain D against A, TM-score 0.58
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 P13569
- Every structure of UniProt P68187
- Elsewhere: RCSB PDB 3GD7 · PDBe 3GD7 · UniProt P13569 · UniProt P68187
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.