MolNFT v1 · #26784 · protein
Crystal structure of the hpce from thermus thermophilus HB8
1WZO: “Crystal structure of the hpce from thermus thermophilus HB8”. X-ray diffraction, 2 ligands (NA, SO4), 15 pockets (best druggability 0.74). MolNFT v1 #26784 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1WZO
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hpce
- EC
- 5.3.3.10
- Ligands
- NA, SO4
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hpce (EC 5.3.3.10) | protein | 236 | 14% helix, 42% strand | — |
| B, D | Hpce (EC 5.3.3.10) | protein | 238 | 13% helix, 42% strand | — |
| C | Hpce (EC 5.3.3.10) | protein | 236 | 14% helix, 42% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.74 | 0.83 | 72 | empty |
| 2 | 507 | 0.73 | 0.82 | 63 | empty |
| 3 | 488 | 0.67 | 0.78 | 55 | empty |
| 4 | 130 | 0.61 | 0.86 | 26 | SO4 |
| 5 | 148 | 0.59 | 0.84 | 27 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1517 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1399 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 648 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 579 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 450 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1WZO · Crystal Structure of the HpcE from Thermus Thermophilus HB8 · 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 1WZO · PDBe 1WZO
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