Research workbench
Cryo-EM reconstruction of quasi-HPV16 complex with H263.A2 Fab
Analyse Cryo-EM reconstruction of quasi-HPV16 complex with H263.A2 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J8W
- Type
- protein
- Length
- 3,013 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H263.A2 light chain; H263.A2 heavy chain; L1
- UniProt
- Q4VRM0
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, J, K, M | H263.A2 light chain | protein | 109 | 3% helix, 48% strand | — |
| H, F, G, I | H263.A2 heavy chain | protein | 118 | 8% helix, 55% strand | — |
| A, B, C, D, E | L1 | protein | 421 | 14% helix, 38% strand | Q4VRM0 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.83 | 0.83 | 103 | empty |
| 2 | 1043 | 0.82 | 0.83 | 112 | empty |
| 3 | 943 | 0.82 | 0.83 | 101 | empty |
| 4 | 1100 | 0.81 | 0.82 | 117 | empty |
| 5 | 850 | 0.67 | 0.74 | 50 | empty |
Interfaces
35 interfaces between chains.
- B–C · 3478 Ų buried · 62 hydrogen bonds · protein-protein
- A–E · 3470 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 3462 Ų buried · 64 hydrogen bonds · protein-protein
- D–E · 3458 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 3455 Ų buried · 66 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3J8W · Cryo-EM reconstruction of quasi-HPV16 complex with H263.A2 Fab · the same entry in another collection · chain L against L, 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
- Every structure of UniProt Q4VRM0
- Elsewhere: RCSB PDB 3J8W · PDBe 3J8W · UniProt Q4VRM0
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