MolNFT v1 · #151214 · protein
Crystal structure of an anti-app-tag Fab
6HGU · Anti-app-tag Fab heavy-chain: “Crystal structure of an anti-app-tag Fab”. X-ray diffraction, 7 pockets (best druggability 0.60). MolNFT v1 #151214 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HGU
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-app-tag Fab heavy-chain; Anti-app-tag Fab light-chain
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-app-tag Fab heavy-chain | protein | 213 | 6% helix, 52% strand | — |
| B, L | Anti-app-tag Fab light-chain | protein | 218 | 6% helix, 51% strand | — |
| H | Anti-app-tag Fab heavy-chain | protein | 215 | 6% helix, 51% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, H, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.60 | 0.74 | 55 | GOL |
| 2 | 384 | 0.58 | 0.75 | 47 | GOL |
| 3 | 106 | 0.48 | 0.80 | 19 | GOL |
| 4 | 91 | 0.45 | 0.79 | 17 | empty |
| 5 | 128 | 0.42 | 0.75 | 26 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1907 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1846 Ų buried · 18 hydrogen bonds · protein-protein
- B–L · 30 Ų buried · 0 hydrogen bonds · protein-protein
- A–L · 18 Ų buried · 0 hydrogen bonds · protein-protein
- A–H · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 6HGU · Crystal Structure of an anti-APP-tag 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 6HGU · PDBe 6HGU
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