MolNFT v1 · #26369 · protein
Crystal structure of C-type lectin cel-I complexed with N-acetyl-D- galactosamine
1WMZ · Lectin cel-I, N-acetyl-D-galactosamine-specific C-type: “Crystal structure of C-type lectin cel-I complexed with N-acetyl-D- galactosamine”. X-ray diffraction, 3 ligands (NGA, A2G, CA), 2 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 1WMZ
- Type
- protein
- Length
- 560 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin cel-I, N-acetyl-D-galactosamine-specific C-type
- UniProt
- Q7M462
- Ligands
- NGA, A2G, CA
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lectin cel-I, N-acetyl-D-galactosamine-specific C-type | protein | 140 | 21% helix, 34% strand | Q7M462 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains A, C, D
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains B
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.68 | 0.94 | 37 | empty |
| 2 | 60 | 0.31 | 0.76 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 846 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 838 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 630 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 593 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 526 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1WMZ · Crystal Structure of C-type Lectin CEL-I complexed with N-acetyl-D-galactosamine · 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
- Every structure of UniProt Q7M462
- Elsewhere: RCSB PDB 1WMZ · PDBe 1WMZ · UniProt Q7M462
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