Research workbench
Crystal structure of a gdsl-like lipase (ALR1529) from nostoc sp. pcc 7120 at 2.02 a resolution
Analyse Crystal structure of a gdsl-like lipase (ALR1529) from nostoc sp. pcc 7120 at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z8H
- Type
- protein
- Length
- 802 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative lipase from the G-D-S-L family
- UniProt
- Q8YWS4
- Ligands
- UNL
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative lipase from the G-D-S-L family | protein | 202 | 47% helix, 17% strand | Q8YWS4 |
| B | Putative lipase from the G-D-S-L family | protein | 199 | 49% helix, 14% strand | Q8YWS4 |
| C | Putative lipase from the G-D-S-L family | protein | 200 | 51% helix, 17% strand | Q8YWS4 |
| D | Putative lipase from the G-D-S-L family | protein | 201 | 50% helix, 14% strand | Q8YWS4 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.80 | 0.82 | 93 | UNL |
| 2 | 435 | 0.70 | 0.81 | 47 | empty |
| 3 | 50 | 0.56 | 0.91 | 25 | empty |
| 4 | 167 | 0.54 | 0.80 | 20 | empty |
| 5 | 92 | 0.39 | 0.76 | 16 | UNL |
Interfaces
6 interfaces between chains.
- C–D · 1124 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1095 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 479 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 431 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 161 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, engineered).
Compared structures
- 1Z8H · CRYSTAL STRUCTURE OF a GDSL-like lipase (ALR1529) FROM NOSTOC SP. PCC 7120 AT 2.02 A… · 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 Q8YWS4
- Elsewhere: RCSB PDB 1Z8H · PDBe 1Z8H · UniProt Q8YWS4
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