MolNFT v1 · #99591 · protein
Unliganded 1 crystal structure of S25-26 Fab
4M7Z · S25-26 Fab (IGG1K) heavy chain: “Unliganded 1 crystal structure of S25-26 Fab”. X-ray diffraction, 2 ligands (NAG, CA), 11 pockets (best druggability 0.65). MolNFT v1 #99591 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4M7Z
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S25-26 Fab (IGG1K) heavy chain; S25-26 Fab (IGG1K) light chain
- Ligands
- NAG, CA
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | S25-26 Fab (IGG1K) heavy chain | protein | 216 | 4% helix, 47% strand | — |
| H | S25-26 Fab (IGG1K) heavy chain | protein | 215 | 4% helix, 47% strand | — |
| C | S25-26 Fab (IGG1K) light chain | protein | 219 | 7% helix, 52% strand | — |
| L | S25-26 Fab (IGG1K) light chain | protein | 218 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, H
- CA · Calcium ion · metal · 3 copies · chains B, H, C, L
- PG4 · Tetraethylene glycol · additive · 8 copies · chains B, C, H, L
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains B, C, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.65 | 0.93 | 18 | empty |
| 2 | 541 | 0.62 | 0.75 | 56 | PG4, PEG |
| 3 | 541 | 0.61 | 0.74 | 54 | PG4 |
| 4 | 321 | 0.56 | 0.76 | 40 | empty |
| 5 | 210 | 0.54 | 0.78 | 36 | empty |
Interfaces
4 interfaces between chains.
- B–C · 2061 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 2009 Ų buried · 16 hydrogen bonds · protein-protein
- B–H · 451 Ų buried · 4 hydrogen bonds · protein-protein
- C–L · 167 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4M7Z · Unliganded 1 crystal structure of S25-26 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 4M7Z · PDBe 4M7Z
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