MolNFT v1 · #124473 · protein
Crystal structure of the GP120 V2 antibody RE505-22 Fab from igh- and igk-humanized mouse
5KG9 · Antibody RE505-22 Fab heavy chain: “Crystal structure of the GP120 V2 antibody RE505-22 Fab from igh- and igk-humanized mouse”. X-ray diffraction, 9 pockets (best druggability 0.60). MolNFT v1 #124473 on GenesisL1: 3D structure…
- PDB
- 5KG9
- Type
- protein
- Length
- 853 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody RE505-22 Fab heavy chain; Antibody RE505-22 Fab light chain
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody RE505-22 Fab heavy chain | protein | 211 | 7% helix, 52% strand | — |
| L, B | Antibody RE505-22 Fab light chain | protein | 218 | 6% helix, 53% strand | — |
| A | Antibody RE505-22 Fab heavy chain | protein | 206 | 6% helix, 50% strand | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.60 | 0.74 | 64 | empty |
| 2 | 543 | 0.60 | 0.74 | 57 | empty |
| 3 | 198 | 0.50 | 0.76 | 41 | empty |
| 4 | 78 | 0.39 | 0.78 | 21 | empty |
| 5 | 99 | 0.37 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1629 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1583 Ų buried · 9 hydrogen bonds · protein-protein
- L–B · 410 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5KG9 · Crystal structure of the gp120 v2 antibody RE505-22 Fab from IGH- and IGK-humanized mouse · the same entry in another collection · chain H against H, 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 5KG9 · PDBe 5KG9
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