MolNFT v1 · #55547 · protein
Crystal structure of geobacillus thermodenitrificans essb extracellular fragment
2YNQ: “Crystal structure of geobacillus thermodenitrificans essb extracellular fragment”. X-ray diffraction, 2 ligands (NA, CL), 8 pockets (best druggability 0.81). MolNFT v1 #55547 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2YNQ
- Type
- protein
- Length
- 600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Essb
- UniProt
- A4IKE6
- Ligands
- NA, CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Essb | protein | 149 | 74% helix, 0% strand | A4IKE6 |
| B | Essb | protein | 151 | 70% helix, 0% strand | A4IKE6 |
| C | Essb | protein | 149 | 77% helix, 0% strand | A4IKE6 |
| D | Essb | protein | 151 | 74% helix, 0% strand | A4IKE6 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, D, B, C
- CL · Chloride ion · ion · 3 copies · chains A, D, B, C
- MLI · Malonate ion · additive · 3 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.81 | 0.82 | 87 | NA, GOL |
| 2 | 211 | 0.48 | 0.75 | 18 | empty |
| 3 | 204 | 0.48 | 0.75 | 32 | CL |
| 4 | 201 | 0.47 | 0.75 | 22 | empty |
| 5 | 115 | 0.45 | 0.78 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1214 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1190 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 746 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 669 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2YNQ · Crystal Structure of Geobacillus thermodenitrificans EssB extracellular fragment · 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 A4IKE6
- Elsewhere: RCSB PDB 2YNQ · PDBe 2YNQ · UniProt A4IKE6
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