Research workbench
Crystal structure of GLVRC01 scfv in complex with anti-idiotype IV8 scfv
Analyse Crystal structure of GLVRC01 scfv in complex with anti-idiotype IV8 scfv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OL7
- Type
- protein
- Length
- 1,851 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IV8 heavy chain; GLVRC01 light chain; GLVRC01 heavy chain; IV8 light chain
- Ligands
- CL
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 10 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K, P | IV8 heavy chain | protein | 117 | 8% helix, 54% strand | — |
| B, N | GLVRC01 light chain | protein | 106 | 3% helix, 52% strand | — |
| C | GLVRC01 heavy chain | protein | 123 | 10% helix, 49% strand | — |
| D | IV8 light chain | protein | 121 | 2% helix, 49% strand | — |
| E | IV8 heavy chain | protein | 120 | 5% helix, 53% strand | — |
| F, L | GLVRC01 light chain | protein | 103 | 3% helix, 52% strand | — |
| H, M | GLVRC01 heavy chain | protein | 120 | 10% helix, 55% strand | — |
| I | GLVRC01 heavy chain | protein | 126 | 10% helix, 52% strand | — |
| J | IV8 light chain | protein | 118 | 3% helix, 51% strand | — |
| O, Q | IV8 light chain | protein | 117 | 3% helix, 51% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains F, K, N, P
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, L, B, E, C, D, F, I, K, H, Q, J, M, N, O, P
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, F, J, K, M, N, O, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.69 | 0.76 | 111 | empty |
| 2 | 658 | 0.64 | 0.75 | 65 | EDO |
| 3 | 184 | 0.60 | 0.82 | 37 | EDO |
| 4 | 181 | 0.58 | 0.81 | 29 | EDO, CL |
| 5 | 116 | 0.55 | 0.83 | 16 | empty |
Interfaces
31 interfaces between chains.
- F–I · 958 Ų buried · 15 hydrogen bonds · protein-protein
- O–P · 867 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 859 Ų buried · 7 hydrogen bonds · protein-protein
- A–Q · 856 Ų buried · 7 hydrogen bonds · protein-protein
- J–K · 844 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6OL7 · Crystal structure of glVRC01 scFv in complex with anti-idiotype iv8 scFv · 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 6OL7 · PDBe 6OL7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.