Research workbench
Crystal structure of 426C.TM4DELTAV1-3 P120
Analyse Crystal structure of 426C.TM4DELTAV1-3 P120 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FA2
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP120
- Ligands
- NAG, MAN, BMA, SCN
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GP120 | protein | 336 | 16% helix, 37% strand | — |
| B | GP120 | protein | 336 | 16% helix, 36% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- SCN · Thiocyanate ion · ion · chains A
- FLC · Citrate anion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.79 | 0.81 | 86 | NAG, FLC |
| 2 | 65 | 0.60 | 0.91 | 19 | SCN |
| 3 | 70 | 0.59 | 0.89 | 18 | empty |
| 4 | 68 | 0.46 | 0.83 | 21 | NAG |
| 5 | 51 | 0.41 | 0.82 | 14 | NAG |
Interfaces
1 interface between chains.
- A–B · 466 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 5FA2 · Crystal structure of 426c.TM4deltaV1-3 p120 · 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
- Elsewhere: RCSB PDB 5FA2 · PDBe 5FA2
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