MolNFT v1 · #154467 · protein + DNA
Crystal structure of yedk with ssdna containing a tetrahydrofuran abasic site
6KBZ · Sos response-associated protein: “Crystal structure of yedk with ssdna containing a tetrahydrofuran abasic site”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.84). MolNFT v1 #154467 on GenesisL1: 3D structure…
- PDB
- 6KBZ
- Type
- protein + DNA
- Length
- 931 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sos response-associated protein; 5'-D (*CP*GP*GP*TP* (3DR) P*GP*AP*TP*TP*C)-3'
- EC
- 3.4.-.-
- UniProt
- A0A2S5ZH06
- Ligands
- MG
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, F | Sos response-associated protein (EC 3.4.-.-) | protein | 226 | 24% helix, 36% strand | A0A2S5ZH06 |
| A, C, E, G | 5'-D (*CP*GP*GP*TP* (3DR) P*GP*AP*TP*TP*C)-3' | dna | 9 | — | — |
| D | Sos response-associated protein (EC 3.4.-.-) | protein | 223 | 23% helix, 35% strand | A0A2S5ZH06 |
| H | Sos response-associated protein (EC 3.4.-.-) | protein | 220 | 22% helix, 35% strand | A0A2S5ZH06 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains B, F, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.84 | 0.85 | 89 | empty |
| 2 | 982 | 0.83 | 0.84 | 75 | empty |
| 3 | 114 | 0.49 | 0.80 | 18 | empty |
| 4 | 72 | 0.44 | 0.82 | 14 | empty |
| 5 | 115 | 0.42 | 0.76 | 25 | empty |
Interfaces
13 interfaces between chains.
- F–E · 927 Ų buried · 21 hydrogen bonds · protein-nucleic
- H–G · 910 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–C · 907 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–A · 900 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–F · 867 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6KBZ · Crystal structure of yedK with ssDNA containing a tetrahydrofuran abasic site · the same entry in another collection · chain B against B, 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 A0A2S5ZH06
- Elsewhere: RCSB PDB 6KBZ · PDBe 6KBZ · UniProt A0A2S5ZH06
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.