MolNFT v1 · #184899 · protein
Crystal structure of glycosyl-enzyme intermediate of RBCEL1 Y201F
7P6J · Endoglucanase: “Crystal structure of glycosyl-enzyme intermediate of RBCEL1 Y201F”. X-ray diffraction, 2 ligands (BGC, GLC), 11 pockets (best druggability 0.67). MolNFT v1 #184899 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7P6J
- Type
- protein
- Length
- 1,274 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase
- EC
- 3.2.1.4
- UniProt
- C1JI15
- Ligands
- BGC, GLC
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Endoglucanase (EC 3.2.1.4) | protein | 318 | 36% helix, 16% strand | C1JI15 |
| B | Endoglucanase (EC 3.2.1.4) | protein | 321 | 36% helix, 16% strand | C1JI15 |
| D | Endoglucanase (EC 3.2.1.4) | protein | 317 | 37% helix, 16% strand | C1JI15 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 23 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.67 | 0.78 | 60 | empty |
| 2 | 336 | 0.66 | 0.81 | 52 | BGC |
| 3 | 210 | 0.57 | 0.80 | 31 | empty |
| 4 | 324 | 0.56 | 0.76 | 33 | empty |
| 5 | 222 | 0.55 | 0.78 | 37 | BGC, GLC |
Interfaces
5 interfaces between chains.
- A–D · 443 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 368 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 310 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 207 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 76 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, glycosylation).
Compared structures
- 7P6J · Crystal structure of glycosyl-enzyme intermediate of RBcel1 Y201F · the same entry in another collection · chain C against C, 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 C1JI15
- Elsewhere: RCSB PDB 7P6J · PDBe 7P6J · UniProt C1JI15
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