MolNFT v1 · #150574 · protein
Crystal structure of CV39L lectin from chromobacterium violaceum at 1.8 a resolution
6GXS: “Crystal structure of CV39L lectin from chromobacterium violaceum at 1.8 a resolution”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.86). MolNFT v1 #150574 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6GXS
- Type
- protein
- Length
- 1,448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CV39L lectin
- UniProt
- Q7NZ70
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CV39L lectin | protein | 362 | 6% helix, 53% strand | Q7NZ70 |
| B | CV39L lectin | protein | 363 | 6% helix, 52% strand | Q7NZ70 |
| C | CV39L lectin | protein | 361 | 6% helix, 52% strand | Q7NZ70 |
| D | CV39L lectin | protein | 362 | 5% helix, 53% strand | Q7NZ70 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, D, B
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.86 | 0.89 | 101 | SO4 |
| 2 | 720 | 0.85 | 0.88 | 81 | SO4 |
| 3 | 98 | 0.41 | 0.77 | 25 | empty |
| 4 | 111 | 0.40 | 0.76 | 30 | empty |
| 5 | 55 | 0.38 | 0.80 | 24 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1674 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1510 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 278 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 141 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6GXS · Crystal structure of CV39L lectin from Chromobacterium violaceum at 1.8 A resolution · 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
- Every structure of UniProt Q7NZ70
- Elsewhere: RCSB PDB 6GXS · PDBe 6GXS · UniProt Q7NZ70
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.