Research workbench
Archael ruvb-like holiday junction helicase
Analyse Archael ruvb-like holiday junction helicase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F4H
- Type
- protein
- Length
- 2,616 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotide binding protein pinc
- UniProt
- C3MQK6
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleotide binding protein pinc | protein | 437 | 34% helix, 28% strand | C3MQK6 |
| B | Nucleotide binding protein pinc | protein | 435 | 34% helix, 28% strand | C3MQK6 |
| C, D, E, F | Nucleotide binding protein pinc | protein | 436 | 35% helix, 29% strand | C3MQK6 |
Ligands and binding sites
- GOL · Glycerol · additive · 21 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.82 | 0.86 | 75 | GOL |
| 2 | 1024 | 0.82 | 0.83 | 89 | EDO, GOL |
| 3 | 742 | 0.81 | 0.85 | 77 | GOL, EDO |
| 4 | 898 | 0.81 | 0.83 | 87 | GOL |
| 5 | 993 | 0.81 | 0.82 | 97 | GOL |
Interfaces
6 interfaces between chains.
- A–B · 2486 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2359 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2295 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 2251 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1984 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5F4H · Archael RuvB-like Holiday junction helicase · 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 C3MQK6
- Elsewhere: RCSB PDB 5F4H · PDBe 5F4H · UniProt C3MQK6
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