MolNFT v1 · #163419 · protein
Anti-tumor antibody 14F7-derived scfv in complex with neugc GM3
6S2I · Scfv C1: “Anti-tumor antibody 14F7-derived scfv in complex with neugc GM3”. X-ray diffraction, 3 ligands (BGC, GAL, NGC), 13 pockets (best druggability 0.76). MolNFT v1 #163419 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6S2I
- Type
- protein
- Length
- 922 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scfv C1
- Ligands
- BGC, GAL, NGC
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Scfv C1 | protein | 125 | 5% helix, 51% strand | — |
| B | Scfv C1 | protein | 106 | 3% helix, 50% strand | — |
| D, F, H | Scfv C1 | protein | 108 | 3% helix, 51% strand | — |
| E | Scfv C1 | protein | 121 | 7% helix, 51% strand | — |
| G | Scfv C1 | protein | 121 | 5% helix, 50% strand | — |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · chains E
- GAL · beta-D-galactopyranose · sugar · chains A, E
- NGC · N-glycolyl-alpha-neuraminic acid · sugar · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.76 | 0.78 | 115 | empty |
| 2 | 156 | 0.48 | 0.77 | 21 | empty |
| 3 | 124 | 0.42 | 0.76 | 21 | empty |
| 4 | 98 | 0.42 | 0.78 | 14 | empty |
| 5 | 87 | 0.37 | 0.76 | 24 | empty |
Interfaces
8 interfaces between chains.
- C–D · 954 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 928 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 917 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 861 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 549 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6S2I · Anti-tumor antibody 14F7-derived scFv in complex with NeuGc Gm3 · the same entry in another collection · chain D against D, 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 6S2I · PDBe 6S2I
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