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Structural basis of HIV-1 tethering to membranes by the BST2-tetherin ectodomain
Analyse Structural basis of HIV-1 tethering to membranes by the BST2-tetherin ectodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X7A
- Type
- protein
- Length
- 605 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bone marrow stromal antigen 2
- UniProt
- Q10589
- Ligands
- NA, MG, CL
- Pockets
- 3 · best druggability 0.29
Structure
x-ray diffraction · 7 distinct chains · 93% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, I, J | Bone marrow stromal antigen 2 | protein | 59 | 95% helix, 0% strand | Q10589 |
| C | Bone marrow stromal antigen 2 | protein | 48 | 96% helix, 0% strand | Q10589 |
| D | Bone marrow stromal antigen 2 | protein | 56 | 93% helix, 0% strand | Q10589 |
| E | Bone marrow stromal antigen 2 | protein | 59 | 95% helix, 0% strand | Q10589 |
| G | Bone marrow stromal antigen 2 | protein | 54 | 91% helix, 0% strand | Q10589 |
| H | Bone marrow stromal antigen 2 | protein | 54 | 89% helix, 0% strand | Q10589 |
| K | Bone marrow stromal antigen 2 | protein | 39 | 90% helix, 0% strand | Q10589 |
Ligands and binding sites
- NA · Sodium ion · metal · 7 copies · chains B, G, E, F, H, I, J
- MG · Magnesium ion · metal · chains I, J
- CL · Chloride ion · ion · 7 copies · chains A, B, G, E, F, H, I
- GOL · Glycerol · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.29 | 0.73 | 16 | empty |
| 2 | 56 | 0.26 | 0.72 | 17 | empty |
| 3 | 51 | 0.23 | 0.71 | 18 | NA, CL |
Interfaces
23 interfaces between chains.
- I–J · 1428 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1414 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1372 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 1260 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 994 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified, 5 disulfide (engineered, disulfide).
Compared structures
- 2X7A · Structural basis of HIV-1 tethering to membranes by the Bst2-tetherin ectodomain · the same entry in another collection · chain K against K, TM-score 1.00
- Q10589 · AlphaFold monomer V2.0 prediction for bone marrow stromal antigen 2 (Q10589) · a predicted model of the same protein · chain E against A, TM-score 0.94
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 Q10589
- Elsewhere: RCSB PDB 2X7A · PDBe 2X7A · UniProt Q10589
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