Research workbench
Crystal structure of unliganded clcf from R.OPACUS 1CP in crystal form 1.
Analyse Crystal structure of unliganded clcf from R.OPACUS 1CP in crystal form 1. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZNJ
- Type
- protein
- Length
- 3,745 residues
- Chains
- 40
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-chloromuconolactone dehalogenase
- UniProt
- Q8G9L0
- Ligands
- CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 4, 6, 8, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, R, S, T, U, V, W, X, Z, a, b, c, d, f | 5-chloromuconolactone dehalogenase | protein | 94 | 35% helix, 33% strand | Q8G9L0 |
| 2 | 5-chloromuconolactone dehalogenase | protein | 93 | 37% helix, 32% strand | Q8G9L0 |
| 3 | 5-chloromuconolactone dehalogenase | protein | 92 | 34% helix, 34% strand | Q8G9L0 |
| 5, 7, e | 5-chloromuconolactone dehalogenase | protein | 92 | 36% helix, 35% strand | Q8G9L0 |
| 9 | 5-chloromuconolactone dehalogenase | protein | 91 | 37% helix, 33% strand | Q8G9L0 |
| Y | 5-chloromuconolactone dehalogenase | protein | 91 | 36% helix, 34% strand | Q8G9L0 |
Ligands and binding sites
- CL · Chloride ion · ion · 40 copies · chains 1, Z, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, R, S, T, U, V, W, X, Y, a, b, c, d, e, f
- EDO · 1,2-ethanediol · additive · 78 copies · chains 1, Z, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, R, S, T, U, V, W, X, Y, a, b, c, d, e, f
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.80 | 0.82 | 110 | empty |
| 2 | 955 | 0.80 | 0.82 | 113 | empty |
| 3 | 1064 | 0.78 | 0.80 | 107 | empty |
| 4 | 1010 | 0.71 | 0.75 | 126 | EDO |
| 5 | 490 | 0.65 | 0.77 | 62 | CL, EDO |
Interfaces
93 interfaces between chains.
- E–F · 1456 Ų buried · 32 hydrogen bonds · protein-protein
- M–N · 1436 Ų buried · 31 hydrogen bonds · protein-protein
- V–W · 1432 Ų buried · 28 hydrogen bonds · protein-protein
- 8–9 · 1430 Ų buried · 27 hydrogen bonds · protein-protein
- T–U · 1429 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3ZNJ · Crystal structure of unliganded ClcF from R.opacus 1CP in crystal form 1. · the same entry in another collection · chain 2 against 2, 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 3ZNJ · PDBe 3ZNJ · UniProt Q8G9L0
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