MolNFT v1 · #138423 · protein
Trae protein in complex with 2-(2-FURYL)ISONICOTINIC acid
5WIP · Conjugal transfer protein: “Trae protein in complex with 2-(2-FURYL)ISONICOTINIC acid”. X-ray diffraction, 1 ligand (XXO), 14 pockets (best druggability 0.55). MolNFT v1 #138423 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5WIP
- Type
- protein
- Length
- 557 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conjugal transfer protein
- UniProt
- Q17U16
- Ligands
- XXO
- Pockets
- 14 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Conjugal transfer protein | protein | 143 | 34% helix, 34% strand | Q17U16 |
| C | Conjugal transfer protein | protein | 136 | 33% helix, 34% strand | Q17U16 |
| D | Conjugal transfer protein | protein | 135 | 39% helix, 36% strand | Q17U16 |
Ligands and binding sites
- XXO · 2-(furan-2-yl)pyridine-4-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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.55 | 0.74 | 52 | empty |
| 2 | 232 | 0.49 | 0.74 | 20 | empty |
| 3 | 140 | 0.47 | 0.77 | 24 | XXO |
| 4 | 161 | 0.46 | 0.76 | 23 | empty |
| 5 | 106 | 0.44 | 0.78 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–D · 615 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 607 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 131 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 104 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WIP · TraE protein in complex with 2-(2-furyl)isonicotinic 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 5WIP · PDBe 5WIP · UniProt Q17U16
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