Research workbench
Crystal structure of the essential E. COLI yeaz protein by mad method using the gadolinium complex "dotma"
Analyse Crystal structure of the essential E. COLI yeaz protein by mad method using the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OKJ
- Type
- protein
- Length
- 879 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA threonylcarbamoyladenosine biosynthesis protein tsab
- EC
- 3.4.-.-
- UniProt
- P76256
- Ligands
- GD3
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA threonylcarbamoyladenosine biosynthesis protein tsab (EC 3.4.-.-) | protein | 219 | 35% helix, 29% strand | P76256 |
| B | TRNA threonylcarbamoyladenosine biosynthesis protein tsab (EC 3.4.-.-) | protein | 222 | 38% helix, 30% strand | P76256 |
| C | TRNA threonylcarbamoyladenosine biosynthesis protein tsab (EC 3.4.-.-) | protein | 218 | 38% helix, 29% strand | P76256 |
| D | TRNA threonylcarbamoyladenosine biosynthesis protein tsab (EC 3.4.-.-) | protein | 220 | 36% helix, 29% strand | P76256 |
Ligands and binding sites
- GD3 · Gadolinium ion · metal · 8 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.73 | 0.79 | 72 | empty |
| 2 | 530 | 0.72 | 0.81 | 58 | empty |
| 3 | 544 | 0.69 | 0.79 | 65 | empty |
| 4 | 110 | 0.40 | 0.76 | 16 | empty |
| 5 | 59 | 0.39 | 0.80 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1048 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 976 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 731 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 408 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1OKJ · crystal structure of the essential E. coli YeaZ protein by MAD method using the… · the same entry in another collection · chain D against D, TM-score 1.00
- P76256 · AlphaFold monomer V2.0 prediction for tRNA threonylcarbamoyladenosine biosynthesis… · 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 P76256
- Elsewhere: RCSB PDB 1OKJ · PDBe 1OKJ · UniProt P76256
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