MolNFT v1 · #138393 · protein
Crystal structure of artb
5WHV · Artb protein: “Crystal structure of artb”. X-ray diffraction, 2 ligands (CA, CL), 5 pockets (best druggability 0.78). MolNFT v1 #138393 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WHV
- Type
- protein
- Length
- 1,199 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Artb protein
- UniProt
- Q404H3
- Ligands
- CA, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, I | Artb protein | protein | 118 | 17% helix, 42% strand | Q404H3 |
| F, G | Artb protein | protein | 119 | 17% helix, 45% strand | Q404H3 |
| H | Artb protein | protein | 125 | 22% helix, 42% strand | Q404H3 |
| J | Artb protein | protein | 128 | 20% helix, 41% strand | Q404H3 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, D, H, B, C, E, F, I, G, J
- CL · Chloride ion · ion · 11 copies · chains A, B, C, D, E, F, G, I, J
- PEG · Di(hydroxyethyl)ether · additive · 21 copies · chains A, C, H, B, E, D, F, I, G, J
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 7 copies · chains A, B, C, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.78 | 0.80 | 99 | PEG, MES |
| 2 | 846 | 0.69 | 0.75 | 62 | PEG, CA |
| 3 | 801 | 0.67 | 0.74 | 34 | PEG |
| 4 | 160 | 0.50 | 0.78 | 27 | CL |
| 5 | 67 | 0.33 | 0.76 | 16 | empty |
Interfaces
17 interfaces between chains.
- F–H · 1129 Ų buried · 22 hydrogen bonds · protein-protein
- I–J · 1084 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1083 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1082 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 1076 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5WHV · Crystal structure of ArtB · 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 Q404H3
- Elsewhere: RCSB PDB 5WHV · PDBe 5WHV · UniProt Q404H3
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