Research workbench
Exbb-exbd complex in MSP1E3D1 nanodisc
Analyse Exbb-exbd complex in MSP1E3D1 nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TYI
- Type
- protein
- Length
- 1,186 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biopolymer transport protein exbb; Biopolymer transport protein exbd
- UniProt
- P0ABU7, P0ABV2
- Ligands
- PEV, PGT
- Pockets
- 20 · best druggability 0.67
Structure
electron microscopy · 6 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biopolymer transport protein exbb | protein | 225 | 81% helix, 0% strand | P0ABU7 |
| B | Biopolymer transport protein exbb | protein | 225 | 84% helix, 0% strand | P0ABU7 |
| C, D | Biopolymer transport protein exbb | protein | 226 | 81% helix, 0% strand | P0ABU7 |
| E | Biopolymer transport protein exbb | protein | 224 | 82% helix, 0% strand | P0ABU7 |
| Y | Biopolymer transport protein exbd | protein | 31 | 61% helix, 0% strand | P0ABV2 |
| Z | Biopolymer transport protein exbd | protein | 29 | 41% helix, 0% strand | P0ABV2 |
Ligands and binding sites
- PEV · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 3 copies · chains B, C, D, E
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.67 | 0.76 | 63 | empty |
| 2 | 684 | 0.66 | 0.75 | 72 | PEV |
| 3 | 55 | 0.61 | 0.92 | 19 | empty |
| 4 | 324 | 0.56 | 0.75 | 37 | empty |
| 5 | 191 | 0.55 | 0.79 | 22 | empty |
Interfaces
14 interfaces between chains.
- C–D · 1666 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1506 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 1502 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1481 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1425 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 P0ABU7
- Every structure of UniProt P0ABV2
- Elsewhere: RCSB PDB 6TYI · PDBe 6TYI · UniProt P0ABU7 · UniProt P0ABV2
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