MolNFT v1 · #125594 · protein
Crystal structure of E.COLI ligt complexed with phosphate
5LDJ · RNA 2',3'-cyclic phosphodiesterase: “Crystal structure of E.COLI ligt complexed with phosphate”. X-ray diffraction, 1 ligand (PO4), 6 pockets (best druggability 0.81). MolNFT v1 #125594 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5LDJ
- Type
- protein
- Length
- 673 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA 2',3'-cyclic phosphodiesterase
- EC
- 3.1.4.-
- UniProt
- A0A140NFI1
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 167 | 28% helix, 38% strand | A0A140NFI1 |
| B | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 175 | 27% helix, 37% strand | A0A140NFI1 |
| C | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 166 | 28% helix, 39% strand | A0A140NFI1 |
| D | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 165 | 27% helix, 39% strand | A0A140NFI1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.81 | 0.82 | 109 | PO4 |
| 2 | 274 | 0.54 | 0.76 | 32 | PO4 |
| 3 | 206 | 0.51 | 0.77 | 33 | empty |
| 4 | 221 | 0.50 | 0.75 | 33 | PO4 |
| 5 | 219 | 0.49 | 0.75 | 28 | empty |
Interfaces
4 interfaces between chains.
- B–C · 928 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 621 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 238 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LDJ · Crystal structure of E.coli LigT complexed with phosphate · 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 A0A140NFI1
- Elsewhere: RCSB PDB 5LDJ · PDBe 5LDJ · UniProt A0A140NFI1
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