MolNFT v1 · #125599 · protein
Crystal structure of E.COLI ligt complexed with 3'-AMP
5LDO · RNA 2',3'-cyclic phosphodiesterase: “Crystal structure of E.COLI ligt complexed with 3'-AMP”. X-ray diffraction, 1 ligand (3AM), 6 pockets (best druggability 0.84). MolNFT v1 #125599 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5LDO
- Type
- protein
- Length
- 678 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
- 3AM
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 174 | 27% helix, 36% strand | A0A140NFI1 |
| B | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 170 | 28% helix, 38% strand | A0A140NFI1 |
| C | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 166 | 28% helix, 38% strand | A0A140NFI1 |
| D | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 168 | 28% helix, 36% strand | A0A140NFI1 |
Ligands and binding sites
- 3AM · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate · ligand · chains A, 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 | 802 | 0.84 | 0.87 | 76 | 3AM |
| 2 | 569 | 0.83 | 0.89 | 73 | empty |
| 3 | 53 | 0.50 | 0.87 | 13 | empty |
| 4 | 121 | 0.45 | 0.78 | 24 | empty |
| 5 | 62 | 0.44 | 0.83 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–C · 805 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 634 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 497 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 479 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5LDO · Crystal structure of E.coli LigT complexed with 3'-AMP · 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 5LDO · PDBe 5LDO · UniProt A0A140NFI1
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