MolNFT v1 · #118534 · protein
The crystal structure of an epoxide hydrolase from streptomyces carzinostaticus subsp. neocarzinostaticus
5F4Z: “The crystal structure of an epoxide hydrolase from streptomyces carzinostaticus subsp. neocarzinostaticus”. X-ray diffraction, 1 ligand (5V4), 20 pockets (best druggability 0.83). MolNFT v1 #118534 on GenesisL1: 3D structure…
- PDB
- 5F4Z
- Type
- protein
- Length
- 1,944 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxide hydrolase
- UniProt
- Q84HB1
- Ligands
- 5V4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Epoxide hydrolase | protein | 388 | 48% helix, 13% strand | Q84HB1 |
| B | Epoxide hydrolase | protein | 390 | 47% helix, 13% strand | Q84HB1 |
| C | Epoxide hydrolase | protein | 387 | 48% helix, 13% strand | Q84HB1 |
| D | Epoxide hydrolase | protein | 391 | 50% helix, 13% strand | Q84HB1 |
Ligands and binding sites
- 5V4 · (1~{R},2~{R})-2,3-dihydro-1~{H}-indene-1,2-diol · ligand · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 7 copies · chains A, B, C, E
- ACT · Acetate ion · additive · 2 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.83 | 0.85 | 76 | 5V4 |
| 2 | 1072 | 0.72 | 0.76 | 107 | ACT, TRS |
| 3 | 551 | 0.69 | 0.78 | 47 | 5V4 |
| 4 | 54 | 0.68 | 0.96 | 16 | 5V4 |
| 5 | 510 | 0.68 | 0.78 | 49 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2572 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2546 Ų buried · 47 hydrogen bonds · protein-protein
- C–E · 474 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 382 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 324 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 modified (engineered).
Compared structures
- 5F4Z · The crystal structure of an epoxide hydrolase from Streptomyces carzinostaticus subsp.… · 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 Q84HB1
- Elsewhere: RCSB PDB 5F4Z · PDBe 5F4Z · UniProt Q84HB1
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