Research workbench
Human RNA ligase rtcb in complex with gmp and CO(II)
Analyse Human RNA ligase rtcb in complex with gmp and CO(II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P3B
- Type
- protein
- Length
- 987 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-splicing ligase rtcb homolog
- EC
- 6.5.1.8
- UniProt
- Q9Y3I0
- Ligands
- 5GP, CO
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-splicing ligase rtcb homolog (EC 6.5.1.8) | protein | 490 | 40% helix, 25% strand | Q9Y3I0 |
| B | RNA-splicing ligase rtcb homolog (EC 6.5.1.8) | protein | 497 | 39% helix, 26% strand | Q9Y3I0 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains B
- ACT · Acetate ion · additive · 2 copies · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.87 | 0.89 | 103 | 5GP, CO, ACT, FMT |
| 2 | 368 | 0.69 | 0.82 | 50 | 5GP, CO |
| 3 | 389 | 0.62 | 0.77 | 50 | empty |
| 4 | 161 | 0.50 | 0.78 | 22 | empty |
| 5 | 82 | 0.41 | 0.79 | 28 | ACT |
Interfaces
1 interface between chains.
- A–B · 1280 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
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 Q9Y3I0
- Elsewhere: RCSB PDB 7P3B · PDBe 7P3B · UniProt Q9Y3I0
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