MolNFT v1 · #15927 · protein
Crystal structure of ybaw probable thioesterase from escherichia COLI
1NJK · Hypothetical protein ybaw: “Crystal structure of ybaw probable thioesterase from escherichia COLI”. X-ray diffraction, 1 ligand (IOD), 7 pockets (best druggability 0.79). MolNFT v1 #15927 on GenesisL1: 3D structure, binding sites…
- PDB
- 1NJK
- Type
- protein
- Length
- 532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein ybaw
- UniProt
- P77712
- Ligands
- IOD
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hypothetical protein ybaw | protein | 133 | 26% helix, 44% strand | P77712 |
Ligands and binding sites
- IOD · Iodide ion · ion · 4 copies · chains C, B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.79 | 0.88 | 40 | empty |
| 2 | 370 | 0.77 | 0.87 | 41 | empty |
| 3 | 100 | 0.76 | 0.98 | 29 | empty |
| 4 | 375 | 0.76 | 0.86 | 47 | IOD |
| 5 | 394 | 0.75 | 0.85 | 49 | IOD |
Interfaces
6 interfaces between chains.
- C–D · 870 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 851 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 654 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 638 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 342 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1NJK · Crystal Structure of YbaW Probable Thioesterase from Escherichia coli · the same entry in another collection · chain D against D, TM-score 1.00
- P77712 · AlphaFold monomer V2.0 prediction for long-chain acyl-CoA thioesterase fadm (P77712) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 P77712
- Elsewhere: RCSB PDB 1NJK · PDBe 1NJK · UniProt P77712
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