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The X-ray crystal structure of the trichoderma reesei family 12 endoglucanase 3, CEL12A, at 1.9 a resolution
Analyse The X-ray crystal structure of the trichoderma reesei family 12 endoglucanase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H8V
- Type
- protein
- Length
- 1,308 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-beta-1,4-glucanase
- EC
- 3.2.1.4
- UniProt
- O00095
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Endo-beta-1,4-glucanase (EC 3.2.1.4) | protein | 218 | 6% helix, 56% strand | O00095 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, E, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.71 | 0.80 | 65 | empty |
| 2 | 366 | 0.67 | 0.81 | 49 | NAG |
| 3 | 396 | 0.67 | 0.80 | 56 | NAG |
| 4 | 362 | 0.64 | 0.80 | 43 | empty |
| 5 | 328 | 0.64 | 0.80 | 52 | empty |
Interfaces
5 interfaces between chains.
- D–E · 856 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 310 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 308 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 288 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 240 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan, 6 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 1H8V · The X-ray Crystal Structure of the Trichoderma reesei Family 12 Endoglucanase 3, Cel12A… · 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 O00095
- Elsewhere: RCSB PDB 1H8V · PDBe 1H8V · UniProt O00095
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