MolNFT v1 · #141768 · protein
The structure of cellobiose 2-epimerase from spirochaeta thermophila dsm 6192
5ZIG: “The structure of cellobiose 2-epimerase from spirochaeta thermophila dsm 6192”. X-ray diffraction, 18 pockets (best druggability 0.65). MolNFT v1 #141768 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZIG
- Type
- protein
- Length
- 1,605 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellobiose 2-epimerase
- EC
- 5.1.3.11
- UniProt
- E0RU15
- Pockets
- 18 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellobiose 2-epimerase (EC 5.1.3.11) | protein | 404 | 56% helix, 11% strand | E0RU15 |
| C | Cellobiose 2-epimerase (EC 5.1.3.11) | protein | 399 | 55% helix, 10% strand | E0RU15 |
| D | Cellobiose 2-epimerase (EC 5.1.3.11) | protein | 398 | 56% helix, 10% strand | E0RU15 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.65 | 0.78 | 37 | empty |
| 2 | 391 | 0.65 | 0.79 | 29 | empty |
| 3 | 381 | 0.64 | 0.78 | 28 | empty |
| 4 | 375 | 0.63 | 0.78 | 33 | empty |
| 5 | 216 | 0.60 | 0.81 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–D · 888 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 854 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 227 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 172 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 161 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5ZIG · The Structure of cellobiose 2-epimerase from Spirochaeta thermophila DSM 6192 · 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 E0RU15
- Elsewhere: RCSB PDB 5ZIG · PDBe 5ZIG · UniProt E0RU15
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