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Crystal structure of pgt 135 Fab in complex with GP120 core protein from HIV-1 strain jr-fl bound to CD4 and 17B Fab
Analyse Crystal structure of pgt 135 Fab in complex with GP120 core protein from HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JM2
- Type
- protein
- Length
- 1,365 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pgt 135 heavy chain; Pgt 135 light chain; 17B light chain; 17B heavy chain; GP120; T-cell…
- UniProt
- P01730
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pgt 135 heavy chain | protein | 227 | 7% helix, 47% strand | — |
| B | Pgt 135 light chain | protein | 214 | 5% helix, 50% strand | — |
| C | 17B light chain | protein | 214 | 6% helix, 47% strand | — |
| D | 17B heavy chain | protein | 220 | 8% helix, 49% strand | — |
| E | GP120 | protein | 315 | 16% helix, 39% strand | — |
| F | T-cell surface glycoprotein CD4 | protein | 175 | 7% helix, 47% strand | P01730 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, E, F
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B, E
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, E
- PG4 · Tetraethylene glycol · additive · chains C, D
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 | 70 | 0.71 | 0.97 | 23 | empty |
| 2 | 160 | 0.66 | 0.87 | 32 | empty |
| 3 | 474 | 0.62 | 0.76 | 55 | empty |
| 4 | 504 | 0.59 | 0.74 | 55 | empty |
| 5 | 405 | 0.59 | 0.75 | 32 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1916 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1728 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1062 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 575 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 435 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4JM2 · Crystal Structure of PGT 135 Fab in Complex with gp120 Core Protein from HIV-1 Strain… · the same entry in another collection · chain C against C, TM-score 1.00
- P01730 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD4 (P01730) · a predicted model of the same protein · chain F against A, TM-score 0.96
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 P01730
- Elsewhere: RCSB PDB 4JM2 · PDBe 4JM2 · UniProt P01730
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