MolNFT v1 · #181572 · protein
Crystal structure of the hcmv pentamer-specific antibody 1-103
7LYV · 1-103 Fab heavy chain: “Crystal structure of the hcmv pentamer-specific antibody 1-103”. X-ray diffraction, 16 pockets (best druggability 0.74). MolNFT v1 #181572 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LYV
- Type
- protein
- Length
- 1,690 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-103 Fab heavy chain; 1-103 Fab light chain
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, C, E | 1-103 Fab heavy chain | protein | 220 | 8% helix, 52% strand | — |
| L, F | 1-103 Fab light chain | protein | 201 | 7% helix, 53% strand | — |
| D | 1-103 Fab light chain | protein | 203 | 6% helix, 53% strand | — |
| A | 1-103 Fab heavy chain | protein | 219 | 9% helix, 51% strand | — |
| B | 1-103 Fab light chain | protein | 206 | 6% helix, 52% strand | — |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.74 | 0.78 | 109 | empty |
| 2 | 671 | 0.63 | 0.74 | 68 | empty |
| 3 | 569 | 0.60 | 0.73 | 61 | empty |
| 4 | 365 | 0.54 | 0.74 | 51 | empty |
| 5 | 263 | 0.53 | 0.76 | 46 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1820 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1798 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1781 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1735 Ų buried · 13 hydrogen bonds · protein-protein
- D–B · 524 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 modified (disulfide, cyclization).
Compared structures
- 7LYV · Crystal structure of the HCMV pentamer-specific antibody 1-103 · 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 7LYV · PDBe 7LYV
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