MolNFT v1 · #125593 · protein
Crystal structure of E.COLI ligt in apo form
5LDI · RNA 2',3'-cyclic phosphodiesterase: “Crystal structure of E.COLI ligt in apo form”. X-ray diffraction, 1 ligand (CL), 8 pockets (best druggability 0.84). MolNFT v1 #125593 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5LDI
- Type
- protein
- Length
- 688 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
- CL
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 175 | 26% helix, 37% strand | A0A140NFI1 |
| B | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 170 | 28% helix, 39% strand | A0A140NFI1 |
| C | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 171 | 27% helix, 37% strand | A0A140NFI1 |
| D | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 172 | 28% helix, 38% strand | A0A140NFI1 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.84 | 0.85 | 91 | empty |
| 2 | 606 | 0.83 | 0.88 | 74 | empty |
| 3 | 111 | 0.49 | 0.81 | 26 | empty |
| 4 | 94 | 0.49 | 0.82 | 24 | empty |
| 5 | 67 | 0.48 | 0.84 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–C · 946 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 614 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 534 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 525 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5LDI · Crystal structure of E.coli LigT in apo form · 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 5LDI · PDBe 5LDI · UniProt A0A140NFI1
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