Research workbench
Crystal structure of TTHA0252 from thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily
Analyse Crystal structure of TTHA0252 from thermus thermophilus HB8, a RNA degradation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DKF
- Type
- protein
- Length
- 1,724 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase superfamily protein
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Metallo-beta-lactamase superfamily protein | protein | 431 | 30% helix, 22% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.76 | 0.82 | 72 | empty |
| 2 | 845 | 0.75 | 0.79 | 64 | empty |
| 3 | 842 | 0.75 | 0.79 | 72 | empty |
| 4 | 862 | 0.75 | 0.79 | 76 | empty |
| 5 | 792 | 0.74 | 0.79 | 60 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1221 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 912 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 736 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 2DKF · Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of… · 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
- Elsewhere: RCSB PDB 2DKF · PDBe 2DKF
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