MolNFT v1 · #32958 · protein
T4 RNA ligase (RNL1) crystal structure
2C5U: “T4 RNA ligase (RNL1) crystal structure”. X-ray diffraction, 4 ligands (APC, CA, MG), 6 pockets (best druggability 0.76). MolNFT v1 #32958 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2C5U
- Type
- protein
- Length
- 750 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA ligase
- EC
- 6.5.1.3
- UniProt
- P00971
- Ligands
- APC, CA, MG, CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA ligase (EC 6.5.1.3) | protein | 375 | 44% helix, 22% strand | P00971 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
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 | 686 | 0.76 | 0.81 | 73 | APC, CA, MG, CL |
| 2 | 664 | 0.76 | 0.82 | 73 | APC, MG, CA, CL |
| 3 | 395 | 0.69 | 0.81 | 40 | empty |
| 4 | 81 | 0.34 | 0.75 | 21 | empty |
| 5 | 56 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 542 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 2C5U · T4 RNA Ligase (Rnl1) Crystal Structure · 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 P00971
- Elsewhere: RCSB PDB 2C5U · PDBe 2C5U · UniProt P00971
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