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Crystal structure of clcf in crystal form 2
Analyse Crystal structure of clcf in crystal form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZNU
- Type
- protein
- Length
- 932 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-chloromuconolactone dehalogenase
- UniProt
- Q8G9L0
- Ligands
- MG, CL
- Pockets
- 18 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | 5-chloromuconolactone dehalogenase | protein | 94 | 34% helix, 33% strand | Q8G9L0 |
| H | 5-chloromuconolactone dehalogenase | protein | 92 | 37% helix, 35% strand | Q8G9L0 |
| I, J | 5-chloromuconolactone dehalogenase | protein | 91 | 37% helix, 34% strand | Q8G9L0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains D, H
- CL · Chloride ion · ion · 14 copies · chains A, D, B, C, G, J, E, F, I, H
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, D, B, C, E, G, F, I, H, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.66 | 0.76 | 68 | EDO |
| 2 | 501 | 0.61 | 0.75 | 61 | EDO, MG |
| 3 | 500 | 0.60 | 0.74 | 64 | EDO |
| 4 | 111 | 0.58 | 0.85 | 18 | CL, EDO |
| 5 | 111 | 0.57 | 0.84 | 18 | CL, EDO |
Interfaces
20 interfaces between chains.
- E–G · 1462 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1454 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1433 Ų buried · 33 hydrogen bonds · protein-protein
- F–I · 1420 Ų buried · 34 hydrogen bonds · protein-protein
- H–J · 1388 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3ZNU · Crystal structure of ClcF in crystal form 2 · 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 Q8G9L0
- Elsewhere: RCSB PDB 3ZNU · PDBe 3ZNU · UniProt Q8G9L0
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