MolNFT v1 · #169828 · protein
Crystal structure of GLVRC01 Fab in complex with anti-idiotypic IV4 Fab
6XOC · IV4 Fab heavy chain: “Crystal structure of GLVRC01 Fab in complex with anti-idiotypic IV4 Fab”. X-ray diffraction, 2 ligands (K, SCN), 9 pockets (best druggability 0.62). MolNFT v1 #169828 on GenesisL1: 3D structure, binding sites…
- PDB
- 6XOC
- Type
- protein
- Length
- 859 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IV4 Fab heavy chain; IV4 Fab light chain; Igl-VRC01 Fab heavy chain; Igl-VRC01 Fab light…
- Ligands
- K, SCN
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IV4 Fab heavy chain | protein | 221 | 10% helix, 51% strand | — |
| B | IV4 Fab light chain | protein | 217 | 7% helix, 52% strand | — |
| H | Igl-VRC01 Fab heavy chain | protein | 214 | 10% helix, 49% strand | — |
| L | Igl-VRC01 Fab light chain | protein | 207 | 6% helix, 52% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 3 copies · chains A
- SCN · Thiocyanate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, H, L
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, L
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.62 | 0.88 | 25 | empty |
| 2 | 325 | 0.56 | 0.76 | 43 | EDO, SCN |
| 3 | 358 | 0.56 | 0.75 | 44 | empty |
| 4 | 248 | 0.56 | 0.77 | 37 | empty |
| 5 | 79 | 0.51 | 0.85 | 17 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 2005 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1597 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 576 Ų buried · 12 hydrogen bonds · protein-protein
- B–L · 284 Ų buried · 1 hydrogen bond · protein-protein
- B–H · 146 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6XOC · Crystal structure of glVRC01 Fab in complex with anti-idiotypic iv4 Fab · the same entry in another collection · chain B against B, 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 6XOC · PDBe 6XOC
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