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Crystal structure of Fab 9H+3L, a putative precursor of the PGT121 family of potent HIV-1 antibodies
Analyse Crystal structure of Fab 9H+3L, a putative precursor of the PGT121 family of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CEY
- Type
- protein
- Length
- 875 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 9H+3L Fab light chain; Antibody 9H+3L Fab heavy chain
- Ligands
- PE7
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody 9H+3L Fab light chain | protein | 211 | 6% helix, 49% strand | — |
| B | Antibody 9H+3L Fab heavy chain | protein | 232 | 4% helix, 50% strand | — |
| C | Antibody 9H+3L Fab light chain | protein | 207 | 6% helix, 49% strand | — |
| D | Antibody 9H+3L Fab heavy chain | protein | 225 | 6% helix, 54% strand | — |
Ligands and binding sites
- PE7 · 1-deoxy-1-thio-heptaethylene glycol · ligand · chains D
- GOL · Glycerol · additive · 2 copies · chains A, C, D
- P6G · Hexaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.70 | 0.78 | 80 | empty |
| 2 | 299 | 0.51 | 0.74 | 36 | empty |
| 3 | 163 | 0.47 | 0.76 | 22 | empty |
| 4 | 164 | 0.45 | 0.75 | 21 | empty |
| 5 | 139 | 0.43 | 0.75 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1941 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1918 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 409 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 378 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 77 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5CEY · Crystal Structure of Fab 9H+3L, a putative precursor of the PGT121 family of potent HIV-1… · 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 5CEY · PDBe 5CEY
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