Research workbench
Crystal structure of metallo-beta-lactamase H8A from Thermotoga maritima
Analyse Crystal structure of metallo-beta-lactamase H8A from Thermotoga maritima in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X2Y
- Type
- protein
- Length
- 681 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.67
- Source
- Thermotoga maritima MSB8
- Molecule
- UPF0173 metal-dependent hydrolase TM_1162
- UniProt
- Q9X0P5
- Ligands
- NI
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.67 · 1 distinct chain · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | UPF0173 metal-dependent hydrolase TM_1162 | protein | 227 | 24% helix, 30% strand | Q9X0P5 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.82 | 0.98 | 27 | empty |
| 2 | 83 | 0.45 | 0.80 | 24 | empty |
| 3 | 182 | 0.44 | 0.74 | 30 | empty |
| 4 | 105 | 0.40 | 0.76 | 22 | empty |
| 5 | 93 | 0.39 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1096 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1093 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1087 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3X2Y · Crystal structure of metallo-beta-lactamase H8A from thermotoga maritima · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X0P5 · AlphaFold monomer V2.0 prediction for UPF0173 metal-dependent hydrolase TM_1162 (Q9X0P5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9X0P5
- Elsewhere: RCSB PDB 3X2Y · PDBe 3X2Y · UniProt Q9X0P5
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