MolNFT v1 · #125453 · protein
Crystal structure of an endoglucanase from penicillium verruculosum in complex with cellobiose
5L9C: “Crystal structure of an endoglucanase from penicillium verruculosum in complex with cellobiose”. X-ray diffraction, 2 ligands (BGC, NAG), 10 pockets (best druggability 0.62). MolNFT v1 #125453 on GenesisL1: 3D structure, binding…
- PDB
- 5L9C
- Type
- protein
- Length
- 1,216 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase
- Ligands
- BGC, NAG
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Endoglucanase | protein | 304 | 38% helix, 18% strand | — |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.62 | 0.76 | 56 | BGC |
| 2 | 531 | 0.62 | 0.75 | 61 | BGC |
| 3 | 209 | 0.55 | 0.79 | 28 | empty |
| 4 | 191 | 0.54 | 0.79 | 27 | empty |
| 5 | 171 | 0.45 | 0.75 | 33 | BGC |
Interfaces
4 interfaces between chains.
- A–B · 456 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 442 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 361 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 325 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5L9C · Crystal structure of an endoglucanase from Penicillium verruculosum in complex with… · 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
- Elsewhere: RCSB PDB 5L9C · PDBe 5L9C
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