Research workbench
Crystal structure of TT0972 protein from thermus thermophilus
Analyse Crystal structure of TT0972 protein from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CZ8
- Type
- protein
- Length
- 537 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TT0972 protein
- Ligands
- FAD, K, PO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | TT0972 protein | protein | 67 | 22% helix, 58% strand | — |
| B, F | TT0972 protein | protein | 66 | 23% helix, 59% strand | — |
| D, E, H | TT0972 protein | protein | 68 | 22% helix, 56% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, C, B, D, E, G, F, H
- K · Potassium ion · metal · 4 copies · chains A, C, D, E, G, H
- PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D, E, F, G, H
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 | 399 | 0.62 | 0.77 | 54 | PO4 |
| 2 | 293 | 0.60 | 0.78 | 48 | PO4 |
| 3 | 77 | 0.36 | 0.77 | 17 | empty |
| 4 | 72 | 0.35 | 0.76 | 18 | FAD |
Interfaces
12 interfaces between chains.
- C–D · 610 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 606 Ų buried · 8 hydrogen bonds · protein-protein
- E–G · 578 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 528 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2CZ8 · Crystal Structure of tt0972 protein from Thermus thermophilus · 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 2CZ8 · PDBe 2CZ8
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