MolNFT v1 · #114647 · protein
HK620 tail needle crystallized at pH 9 (crystal form II)
5BVZ · DNA stabilization protein: “HK620 tail needle crystallized at pH 9 (crystal form II)”. X-ray diffraction, 2 ligands (CA, CL), 6 pockets (best druggability 0.62). MolNFT v1 #114647 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5BVZ
- Type
- protein
- Length
- 1,080 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA stabilization protein
- UniProt
- Q9AYZ3
- Ligands
- CA, CL
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | DNA stabilization protein | protein | 180 | 62% helix, 10% strand | Q9AYZ3 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D, E, F
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 | 361 | 0.62 | 0.78 | 34 | empty |
| 2 | 318 | 0.59 | 0.78 | 33 | empty |
| 3 | 125 | 0.50 | 0.80 | 20 | empty |
| 4 | 138 | 0.49 | 0.79 | 18 | empty |
| 5 | 185 | 0.45 | 0.74 | 28 | empty |
Interfaces
11 interfaces between chains.
- A–B · 4204 Ų buried · 91 hydrogen bonds · protein-protein
- B–C · 4201 Ų buried · 79 hydrogen bonds · protein-protein
- E–F · 4200 Ų buried · 90 hydrogen bonds · protein-protein
- D–E · 4167 Ų buried · 82 hydrogen bonds · protein-protein
- D–F · 4156 Ų buried · 85 hydrogen bonds · protein-protein
Compared structures
- 5BVZ · HK620 Tail Needle crystallized at pH 9 (Crystal form II) · 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 Q9AYZ3
- Elsewhere: RCSB PDB 5BVZ · PDBe 5BVZ · UniProt Q9AYZ3
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