MolNFT v1 · #125601 · protein
Crystal structure of E.COLI ligt complexed with NADP+
5LDQ · RNA 2',3'-cyclic phosphodiesterase: “Crystal structure of E.COLI ligt complexed with NADP+”. X-ray diffraction, 3 ligands (NAP, CL, PO4), 6 pockets (best druggability 0.80). MolNFT v1 #125601 on GenesisL1: 3D structure, binding…
- PDB
- 5LDQ
- Type
- protein
- Length
- 691 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
- NAP, CL, PO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 175 | 27% helix, 38% strand | A0A140NFI1 |
| B | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 169 | 27% helix, 38% strand | A0A140NFI1 |
| D | RNA 2',3'-cyclic phosphodiesterase (EC 3.1.4.-) | protein | 172 | 27% helix, 38% strand | A0A140NFI1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains D
- 1PE · Pentaethylene glycol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.80 | 0.87 | 45 | NAP, CL |
| 2 | 565 | 0.75 | 0.83 | 53 | NAP, CL |
| 3 | 413 | 0.61 | 0.76 | 40 | NAP |
| 4 | 304 | 0.56 | 0.76 | 38 | NAP |
| 5 | 210 | 0.49 | 0.75 | 27 | CL, 1PE |
Interfaces
3 interfaces between chains.
- A–B · 859 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 602 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 81 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LDQ · Crystal structure of E.coli LigT complexed with NADP+ · 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 5LDQ · PDBe 5LDQ · UniProt A0A140NFI1
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