MolNFT v1 · #134425 · protein
HIV GP140 trimer MD39-10MUTA in complex with fabs PGT124 and 35022
5T3S · Envelope glycoprotein GP160: “HIV GP140 trimer MD39-10MUTA in complex with fabs PGT124 and 35022”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.63). MolNFT v1 #134425 on GenesisL1: 3D structure…
- PDB
- 5T3S
- Type
- protein
- Length
- 1,452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Fab PGT124 light chain; Fab PGT124 heavy chain; Fab 35022…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 442 | 13% helix, 37% strand | Q2N0S6 |
| B | Envelope glycoprotein GP160 | protein | 122 | 57% helix, 6% strand | Q2N0S6 |
| L | Fab PGT124 light chain | protein | 210 | 7% helix, 46% strand | — |
| H | Fab PGT124 heavy chain | protein | 225 | 4% helix, 52% strand | — |
| D | Fab 35022 heavy chain | protein | 240 | 8% helix, 50% strand | — |
| E | Fab 35022 light chain | protein | 213 | 7% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains G, D, B, H, E
- MAN · alpha-D-mannopyranose · sugar · 19 copies · chains G, D, E, L, H
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains G, D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.63 | 0.81 | 33 | empty |
| 2 | 177 | 0.62 | 0.83 | 36 | NAG |
| 3 | 148 | 0.62 | 0.85 | 26 | empty |
| 4 | 456 | 0.58 | 0.74 | 61 | empty |
| 5 | 409 | 0.55 | 0.73 | 55 | empty |
Interfaces
8 interfaces between chains.
- G–B · 2501 Ų buried · 22 hydrogen bonds · protein-protein
- L–H · 1905 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1770 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 423 Ų buried · 8 hydrogen bonds · protein-protein
- G–D · 358 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 17 glycan (disulfide, N-glycosylation).
Compared structures
- 5T3S · HIV gp140 trimer MD39-10MUTA in complex with Fabs PGT124 and 35022 · 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 Q2N0S6
- Elsewhere: RCSB PDB 5T3S · PDBe 5T3S · UniProt Q2N0S6
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