Research workbench
Crystal structure of mvl bound to MAN3GLCNAC2
Analyse Crystal structure of mvl bound to MAN3GLCNAC2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZHS
- Type
- protein
- Length
- 904 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannan-binding lectin
- Ligands
- NAG, MAN, BMA, PO4
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Mannan-binding lectin | protein | 113 | 24% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, C, B, D, E, F, G, H
- MAN · alpha-D-mannopyranose · sugar · 32 copies · chains A, B, C, D, E, F, G, H
- BMA · beta-D-mannopyranose · sugar · 16 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · 2 copies · chains G
- EDO · 1,2-ethanediol · additive · 26 copies · chains A, B, E, C, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.84 | 0.85 | 90 | NAG, EDO |
| 2 | 1183 | 0.83 | 0.84 | 98 | NAG, EDO |
| 3 | 1173 | 0.82 | 0.83 | 138 | EDO |
| 4 | 356 | 0.75 | 0.86 | 64 | EDO |
| 5 | 228 | 0.74 | 0.89 | 46 | EDO |
Interfaces
15 interfaces between chains.
- G–H · 1985 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1982 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1972 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1966 Ų buried · 12 hydrogen bonds · protein-protein
- D–G · 236 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1ZHS · Crystal structure of MVL bound to Man3GlcNAc2 · the same entry in another collection · chain E against E, 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 1ZHS · PDBe 1ZHS
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