Research workbench
Unliganded 3 crystal structure of S25-26 Fab
Analyse Unliganded 3 crystal structure of S25-26 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MA1
- Type
- protein
- Length
- 1,309 residues
- Chains
- 6
- 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, MAN, BMA, FUC, GAL, GLA, K
- Pockets
- 19 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, H | S25-26 Fab (IGG1K) heavy chain | protein | 218 | 7% helix, 50% strand | — |
| E | S25-26 Fab (IGG1K) heavy chain | protein | 216 | 4% helix, 47% strand | — |
| C, F, L | S25-26 Fab (IGG1K) light chain | protein | 219 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, E, H
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies
- GAL · beta-D-galactopyranose · sugar
- GLA · alpha-D-galactopyranose · sugar
- K · Potassium ion · metal · chains L
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.72 | 0.79 | 58 | empty |
| 2 | 325 | 0.59 | 0.77 | 30 | empty |
| 3 | 363 | 0.55 | 0.74 | 48 | empty |
| 4 | 205 | 0.53 | 0.78 | 29 | empty |
| 5 | 156 | 0.52 | 0.79 | 24 | empty |
Interfaces
7 interfaces between chains.
- E–F · 2065 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2057 Ų buried · 23 hydrogen bonds · protein-protein
- H–L · 2032 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 532 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 427 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4MA1 · Unliganded 3 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 4MA1 · PDBe 4MA1
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