MolNFT v1 · #135963 · protein
Crystal structure of 354NC37 Fab in complex with HIV-1 clade ae strain 93TH057 GP120
5UEM · Clade A/E 93TH057 HIV-1 GP120 core: “Crystal structure of 354NC37 Fab in complex with HIV-1 clade ae strain 93TH057 GP120”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 7 pockets (best druggability 0.77). MolNFT v1 #135963 on…
- PDB
- 5UEM
- Type
- protein
- Length
- 784 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; 354NC37 Fab heavy chain; 354NC37 Fab light chain
- UniProt
- A0A0M3KKW9
- Ligands
- NAG, MAN, BMA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 341 | 18% helix, 36% strand | A0A0M3KKW9 |
| H | 354NC37 Fab heavy chain | protein | 230 | 9% helix, 50% strand | — |
| L | 354NC37 Fab light chain | protein | 213 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains G, L
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains G
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains G
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.77 | 0.85 | 63 | NAG |
| 2 | 62 | 0.61 | 0.92 | 24 | empty |
| 3 | 498 | 0.61 | 0.75 | 48 | empty |
| 4 | 213 | 0.57 | 0.79 | 35 | empty |
| 5 | 78 | 0.48 | 0.83 | 22 | NAG |
Interfaces
3 interfaces between chains.
- H–L · 1836 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 791 Ų buried · 11 hydrogen bonds · protein-protein
- G–L · 169 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 5UEM · Crystal structure of 354NC37 Fab in complex with HIV-1 clade AE strain 93TH057 gp120 · the same entry in another collection · chain G against G, 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 A0A0M3KKW9
- Elsewhere: RCSB PDB 5UEM · PDBe 5UEM · UniProt A0A0M3KKW9
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