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The first crystal structure of an archaeal metallo-beta-lactamase superfamily protein; ST1585 from sulfolobus tokodaii
Analyse The first crystal structure of an archaeal metallo-beta-lactamase superfamily… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ADR
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein ST1585
- UniProt
- Q970L2
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein ST1585 | protein | 259 | 34% helix, 23% strand | Q970L2 |
| B | Putative uncharacterized protein ST1585 | protein | 256 | 32% helix, 23% strand | Q970L2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.82 | 0.86 | 78 | EDO |
| 2 | 203 | 0.66 | 0.84 | 35 | empty |
| 3 | 188 | 0.45 | 0.74 | 21 | EDO |
| 4 | 56 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 666 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 3ADR · The first crystal structure of an archaeal metallo-beta-lactamase superfamily protein… · the same entry in another collection · chain A against A, TM-score 1.00
- Q970L2 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase fold- containing protein… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q970L2
- Elsewhere: RCSB PDB 3ADR · PDBe 3ADR · UniProt Q970L2
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