MolNFT v1 · #135859 · protein
Crystal structure of human C1S in complex with inhibitor gigastasin
5UBM · Complement C1S subcomponent: “Crystal structure of human C1S in complex with inhibitor gigastasin”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.77). MolNFT v1 #135859 on GenesisL1: 3D structure, binding sites…
- PDB
- 5UBM
- Type
- protein
- Length
- 495 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C1S subcomponent; Gigastasin
- EC
- 3.4.21.42
- UniProt
- P09871
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C1S subcomponent (EC 3.4.21.42) | protein | 233 | 13% helix, 39% strand | P09871 |
| B | Complement C1S subcomponent (EC 3.4.21.42) | protein | 147 | 0% helix, 37% strand | P09871 |
| I | Gigastasin | protein | 115 | 3% helix, 26% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.77 | 0.81 | 94 | empty |
| 2 | 197 | 0.44 | 0.73 | 30 | empty |
| 3 | 54 | 0.35 | 0.79 | 17 | empty |
| 4 | 58 | 0.27 | 0.73 | 17 | empty |
| 5 | 50 | 0.25 | 0.73 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–I · 1450 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 896 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 modified, 1 glycan (disulfide, sulfation, N-glycosylation).
Compared structures
- 5UBM · Crystal structure of human C1s in complex with inhibitor gigastasin · the same entry in another collection · chain A against A, TM-score 1.00
- P09871 · AlphaFold monomer V2.0 prediction for complement C1S subcomponent (P09871) · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P09871
- Elsewhere: RCSB PDB 5UBM · PDBe 5UBM · UniProt P09871
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