Research workbench
Crystal structure of hypothetical protein yjjx from escherichia COLI
Analyse Crystal structure of hypothetical protein yjjx from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U5W
- Type
- protein
- Length
- 1,362 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical UPF0244 protein yjjx
- UniProt
- P39411
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical UPF0244 protein yjjx | protein | 162 | 44% helix, 23% strand | P39411 |
| B, D, E | Hypothetical UPF0244 protein yjjx | protein | 172 | 47% helix, 22% strand | P39411 |
| C | Hypothetical UPF0244 protein yjjx | protein | 174 | 45% helix, 21% strand | P39411 |
| F | Hypothetical UPF0244 protein yjjx | protein | 172 | 45% helix, 21% strand | P39411 |
| G | Hypothetical UPF0244 protein yjjx | protein | 168 | 40% helix, 21% strand | P39411 |
| H | Hypothetical UPF0244 protein yjjx | protein | 170 | 43% helix, 22% strand | P39411 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, D, C, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.79 | 0.81 | 106 | SO4 |
| 2 | 1180 | 0.76 | 0.78 | 91 | empty |
| 3 | 358 | 0.66 | 0.80 | 40 | SO4 |
| 4 | 236 | 0.63 | 0.82 | 36 | SO4 |
| 5 | 284 | 0.63 | 0.80 | 41 | SO4 |
Interfaces
11 interfaces between chains.
- C–D · 1498 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1493 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1464 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1444 Ų buried · 15 hydrogen bonds · protein-protein
- E–G · 1069 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1U5W · Crystal structure of hypothetical protein yjjX from Escherichia coli · the same entry in another collection · chain D against D, TM-score 1.00
- P39411 · AlphaFold monomer V2.0 prediction for INOSINE/XANTHOSINE triphosphatase (P39411) · a predicted model of the same protein · chain H against A, TM-score 0.99
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 P39411
- Elsewhere: RCSB PDB 1U5W · PDBe 1U5W · UniProt P39411
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