MolNFT v1 · #12195 · protein
Complex of dc-sign and GLCNAC2MAN3
1K9I · Mdc-SIGN1B type I isoform: “Complex of dc-sign and GLCNAC2MAN3”. X-ray diffraction, 3 ligands (MAN, NAG, CA), 16 pockets (best druggability 0.77). MolNFT v1 #12195 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1K9I
- Type
- protein
- Length
- 1,283 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mdc-SIGN1B type I isoform
- Ligands
- MAN, NAG, CA
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, I, J | Mdc-SIGN1B type I isoform | protein | 128 | 21% helix, 30% strand | — |
| D | Mdc-SIGN1B type I isoform | protein | 132 | 22% helix, 30% strand | — |
| H | Mdc-SIGN1B type I isoform | protein | 127 | 22% helix, 31% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A, J, C, I, D, F, E, B, G, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, J, C, I, D, F, B, E, G, H
- CA · Calcium ion · metal · 30 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.77 | 0.81 | 91 | MAN, NAG |
| 2 | 949 | 0.76 | 0.79 | 102 | MAN, NAG, CA |
| 3 | 430 | 0.68 | 0.80 | 67 | NAG |
| 4 | 110 | 0.51 | 0.81 | 28 | empty |
| 5 | 93 | 0.47 | 0.81 | 22 | empty |
Interfaces
18 interfaces between chains.
- A–B · 675 Ų buried · 10 hydrogen bonds · protein-protein
- D–I · 674 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 669 Ų buried · 13 hydrogen bonds · protein-protein
- E–J · 668 Ų buried · 12 hydrogen bonds · protein-protein
- B–G · 409 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide (disulfide).
Compared structures
- 1K9I · Complex of DC-SIGN and GlcNAc2Man3 · 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
- Elsewhere: RCSB PDB 1K9I · PDBe 1K9I
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