MolNFT v1 · #114881 · protein
Constitutively active sin recombinase catalytic domain reveals two rotational intermediates
5C31 · Sin, putative plasmid resolvase dimer: “Constitutively active sin recombinase catalytic domain reveals two rotational intermediates”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.81). MolNFT v1 #114881 on…
- PDB
- 5C31
- Type
- protein
- Length
- 1,501 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sin, putative plasmid resolvase dimer
- UniProt
- P20384
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, I, K | Sin, putative plasmid resolvase dimer | protein | 126 | 46% helix, 15% strand | P20384 |
| C, D, E, F, H, J, L | Sin, putative plasmid resolvase dimer | protein | 125 | 46% helix, 15% strand | P20384 |
| G | Sin, putative plasmid resolvase dimer | protein | 122 | 45% helix, 16% strand | P20384 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.81 | 0.82 | 101 | empty |
| 2 | 954 | 0.74 | 0.77 | 88 | SO4 |
| 3 | 406 | 0.67 | 0.80 | 45 | empty |
| 4 | 302 | 0.66 | 0.82 | 35 | empty |
| 5 | 96 | 0.64 | 0.89 | 18 | empty |
Interfaces
25 interfaces between chains.
- C–D · 933 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 925 Ų buried · 13 hydrogen bonds · protein-protein
- K–L · 915 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 904 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 878 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 84 modified (engineered).
Compared structures
- 5C31 · Constitutively active Sin recombinase catalytic domain reveals two rotational… · the same entry in another collection · chain L against L, 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 P20384
- Elsewhere: RCSB PDB 5C31 · PDBe 5C31 · UniProt P20384
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