Research workbench
Trae protein in complex with 4-(1H-pyrrol-1-YL)PYRIDINE-2-carboxylic acid
Analyse Trae protein in complex with 4-(1H-pyrrol-1-YL)PYRIDINE-2-carboxylic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WIO
- Type
- protein
- Length
- 558 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conjugal transfer protein
- UniProt
- Q17U16
- Ligands
- XXE
- Pockets
- 14 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conjugal transfer protein | protein | 143 | 35% helix, 34% strand | Q17U16 |
| B | Conjugal transfer protein | protein | 142 | 32% helix, 31% strand | Q17U16 |
| C | Conjugal transfer protein | protein | 139 | 25% helix, 33% strand | Q17U16 |
| D | Conjugal transfer protein | protein | 134 | 22% helix, 33% strand | Q17U16 |
Ligands and binding sites
- XXE · 4-(1H-pyrrol-1-yl)pyridine-2-carboxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.47 | 0.75 | 22 | empty |
| 2 | 155 | 0.46 | 0.76 | 22 | empty |
| 3 | 227 | 0.46 | 0.73 | 33 | empty |
| 4 | 146 | 0.45 | 0.76 | 24 | empty |
| 5 | 134 | 0.43 | 0.76 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–C · 624 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 547 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 163 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 109 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WIO · TraE protein in complex with 4-(1H-pyrrol-1-yl)pyridine-2-carboxylic acid · 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
- Every structure of UniProt Q17U16
- Elsewhere: RCSB PDB 5WIO · PDBe 5WIO · UniProt Q17U16
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