Research workbench
Crystal structure of putative pectinase (YP_001304412.1) from parabacteroides distasonis atcc 8503 at 2.30 a resolution
Analyse Crystal structure of putative pectinase (YP_001304412.1) from parabacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LYC
- Type
- protein
- Length
- 3,827 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pectinase
- UniProt
- A6LGH6
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 3% helix, 69% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, H, I, K, M | Putative pectinase | protein | 241 | 3% helix, 76% strand | A6LGH6 |
| B | Putative pectinase | protein | 237 | 4% helix, 69% strand | A6LGH6 |
| D, O | Putative pectinase | protein | 240 | 3% helix, 69% strand | A6LGH6 |
| F | Putative pectinase | protein | 239 | 4% helix, 68% strand | A6LGH6 |
| J | Putative pectinase | protein | 238 | 4% helix, 69% strand | A6LGH6 |
| L | Putative pectinase | protein | 235 | 3% helix, 69% strand | A6LGH6 |
| N | Putative pectinase | protein | 238 | 4% helix, 68% strand | A6LGH6 |
| P | Putative pectinase | protein | 232 | 3% helix, 69% strand | A6LGH6 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.80 | 0.83 | 114 | empty |
| 2 | 719 | 0.78 | 0.83 | 68 | empty |
| 3 | 588 | 0.75 | 0.83 | 59 | empty |
| 4 | 311 | 0.72 | 0.85 | 52 | empty |
| 5 | 66 | 0.69 | 0.95 | 18 | empty |
Interfaces
44 interfaces between chains.
- E–F · 1070 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1026 Ų buried · 29 hydrogen bonds · protein-protein
- M–N · 1018 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 985 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 969 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 80 modified (engineered).
Compared structures
- 3LYC · Crystal structure of Putative pectinase (YP_001304412.1) from Parabacteroides distasonis… · 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 A6LGH6
- Elsewhere: RCSB PDB 3LYC · PDBe 3LYC · UniProt A6LGH6
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