MolNFT v1 · #164790 · protein
Crystal structure of an endoglucanase D213A from penicillium verruculosum
6T9G: “Crystal structure of an endoglucanase D213A from penicillium verruculosum”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.60). MolNFT v1 #164790 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6T9G
- Type
- protein
- Length
- 1,217 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase
- UniProt
- A0A1U7Q1U3
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Endoglucanase | protein | 305 | 36% helix, 18% strand | A0A1U7Q1U3 |
| B | Endoglucanase | protein | 303 | 36% helix, 18% strand | A0A1U7Q1U3 |
| D | Endoglucanase | protein | 304 | 37% helix, 19% strand | A0A1U7Q1U3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.60 | 0.74 | 65 | empty |
| 2 | 420 | 0.60 | 0.76 | 48 | empty |
| 3 | 152 | 0.53 | 0.80 | 28 | empty |
| 4 | 103 | 0.40 | 0.76 | 26 | empty |
| 5 | 88 | 0.37 | 0.76 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–D · 464 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 462 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 217 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6T9G · Crystal structure of an endoglucanase D213A from penicillium verruculosum · 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 A0A1U7Q1U3
- Elsewhere: RCSB PDB 6T9G · PDBe 6T9G · UniProt A0A1U7Q1U3
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