MolNFT v1 · #135920 · protein
Structure of the N-terminal domain of lipoprotein-releasing system transmembrane protein lole from acinetobacter baumannii
5UDF: “Structure of the N-terminal domain of lipoprotein-releasing system transmembrane protein lole from…”. X-ray diffraction, 7 pockets (best druggability 0.83). MolNFT v1 #135920 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5UDF
- Type
- protein
- Length
- 815 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein-releasing system transmembrane protein lole
- UniProt
- A0A0D5YFP2
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein-releasing system transmembrane protein lole | protein | 209 | 29% helix, 39% strand | A0A0D5YFP2 |
| B | Lipoprotein-releasing system transmembrane protein lole | protein | 198 | 29% helix, 40% strand | A0A0D5YFP2 |
| C | Lipoprotein-releasing system transmembrane protein lole | protein | 205 | 29% helix, 41% strand | A0A0D5YFP2 |
| D | Lipoprotein-releasing system transmembrane protein lole | protein | 203 | 28% helix, 40% strand | A0A0D5YFP2 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.83 | 0.84 | 85 | empty |
| 2 | 294 | 0.72 | 0.85 | 39 | empty |
| 3 | 411 | 0.64 | 0.78 | 38 | empty |
| 4 | 153 | 0.40 | 0.73 | 28 | empty |
| 5 | 93 | 0.38 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1540 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 801 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 759 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 556 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 243 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5UDF · Structure of the N-terminal domain of lipoprotein-releasing system transmembrane protein… · 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 A0A0D5YFP2
- Elsewhere: RCSB PDB 5UDF · PDBe 5UDF · UniProt A0A0D5YFP2
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