MolNFT v1 · #186438 · protein
Crystal structure of FH1 Fab bound to HXB2 HIV-1 GP120 core
7RDW · Glycoprotein 120: “Crystal structure of FH1 Fab bound to HXB2 HIV-1 GP120 core”. X-ray diffraction, 4 ligands (NAG, BMA, NH4), 20 pockets (best druggability 0.80). MolNFT v1 #186438 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7RDW
- Type
- protein
- Length
- 2,973 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein 120; FH1 Fab heavy chain; FH1 Fab light chain
- Ligands
- NAG, BMA, NH4, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 12 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Glycoprotein 120 | protein | 326 | 16% helix, 36% strand | — |
| D | Glycoprotein 120 | protein | 329 | 16% helix, 34% strand | — |
| G | FH1 Fab heavy chain | protein | 210 | 8% helix, 52% strand | — |
| H | FH1 Fab heavy chain | protein | 209 | 7% helix, 49% strand | — |
| I | FH1 Fab light chain | protein | 209 | 7% helix, 48% strand | — |
| L | FH1 Fab light chain | protein | 208 | 6% helix, 47% strand | — |
| M | Glycoprotein 120 | protein | 328 | 16% helix, 34% strand | — |
| N | Glycoprotein 120 | protein | 329 | 16% helix, 32% strand | — |
| Q | FH1 Fab heavy chain | protein | 212 | 6% helix, 51% strand | — |
| R | FH1 Fab light chain | protein | 205 | 5% helix, 46% strand | — |
| U | FH1 Fab heavy chain | protein | 208 | 5% helix, 49% strand | — |
| V | FH1 Fab light chain | protein | 200 | 7% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains C, D, M, N, L, R
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains C, D, M
- NH4 · Ammonium ion · ion · 4 copies · chains C, D, G, I
- SO4 · Sulfate ion · ion · 3 copies · chains C, D, M, N
- EDO · 1,2-ethanediol · additive · 6 copies · chains C, D, H, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.80 | 0.81 | 126 | NAG, EDO, SO4 |
| 2 | 339 | 0.73 | 0.85 | 60 | empty |
| 3 | 618 | 0.69 | 0.78 | 97 | empty |
| 4 | 104 | 0.68 | 0.91 | 27 | empty |
| 5 | 259 | 0.68 | 0.85 | 51 | empty |
Interfaces
18 interfaces between chains.
- Q–R · 1643 Ų buried · 8 hydrogen bonds · protein-protein
- H–L · 1544 Ų buried · 12 hydrogen bonds · protein-protein
- U–V · 1344 Ų buried · 10 hydrogen bonds · protein-protein
- G–I · 1285 Ų buried · 5 hydrogen bonds · protein-protein
- C–Q · 735 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 32 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 7RDW · Crystal Structure of FH1 Fab bound to HXb2 HIV-1 gp120 core · the same entry in another collection · chain C against C, 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 7RDW · PDBe 7RDW
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