Research workbench
A carbohydrate esterase family 15 (CE15) glucuronoyl esterase from caldicellulosiruptor kristjansonii
Analyse A carbohydrate esterase family 15 (CE15) glucuronoyl esterase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NN3
- Type
- protein
- Length
- 1,507 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylanase
- EC
- 3.2.1.8
- UniProt
- E4S6E9
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-xylanase (EC 3.2.1.8) | protein | 383 | 34% helix, 20% strand | E4S6E9 |
| B | Beta-xylanase (EC 3.2.1.8) | protein | 371 | 34% helix, 22% strand | E4S6E9 |
| C | Beta-xylanase (EC 3.2.1.8) | protein | 372 | 35% helix, 22% strand | E4S6E9 |
| D | Beta-xylanase (EC 3.2.1.8) | protein | 381 | 34% helix, 20% strand | E4S6E9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B, D, C
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, B, C
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.81 | 0.83 | 116 | PGE, EDO |
| 2 | 129 | 0.59 | 0.85 | 25 | empty |
| 3 | 308 | 0.57 | 0.77 | 32 | empty |
| 4 | 196 | 0.57 | 0.80 | 38 | empty |
| 5 | 67 | 0.49 | 0.84 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1126 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 944 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 918 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 379 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7NN3 · A carbohydrate esterase family 15 (CE15) glucuronoyl esterase from Caldicellulosiruptor… · 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 E4S6E9
- Elsewhere: RCSB PDB 7NN3 · PDBe 7NN3 · UniProt E4S6E9
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