MolNFT v1 · #178788 · protein
Crystal structure of GLVRC01 Fab in complex with anti-idiotype IV9 Fab
7JLN · IV9 heavy chain: “Crystal structure of GLVRC01 Fab in complex with anti-idiotype IV9 Fab”. X-ray diffraction, 2 ligands (NA, NH4), 7 pockets (best druggability 0.65). MolNFT v1 #178788 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7JLN
- Type
- protein
- Length
- 857 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IV9 heavy chain; IV9 light chain; GLVRC01 heavy chain; GLVRC01 light chain
- Ligands
- NA, NH4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IV9 heavy chain | protein | 215 | 8% helix, 53% strand | — |
| B | IV9 light chain | protein | 218 | 5% helix, 51% strand | — |
| H | GLVRC01 heavy chain | protein | 216 | 7% helix, 50% strand | — |
| L | GLVRC01 light chain | protein | 208 | 6% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.65 | 0.75 | 52 | empty |
| 2 | 65 | 0.53 | 0.87 | 21 | empty |
| 3 | 286 | 0.52 | 0.74 | 41 | empty |
| 4 | 119 | 0.37 | 0.74 | 24 | empty |
| 5 | 94 | 0.37 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1833 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1721 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 547 Ų buried · 7 hydrogen bonds · protein-protein
- B–H · 435 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 7JLN · Crystal structure of glVRC01 Fab in complex with anti-idiotype iv9 Fab · 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 7JLN · PDBe 7JLN
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