Research workbench
Lysyl-adenylate form of human ligiv catalytic domain with bound DNA substrate in open conformation
Analyse Lysyl-adenylate form of human ligiv catalytic domain with bound DNA substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BKF
- Type
- protein + DNA
- Length
- 598 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase 4; DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3'); DNA (5'…
- EC
- 6.5.1.1
- UniProt
- P49917
- Ligands
- AMP
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase 4 (EC 6.5.1.1) | protein | 562 | 37% helix, 22% strand | P49917 |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3') | dna | 11 | — | — |
| T | DNA (5'- D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') | dna | 18 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3') | dna | 7 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.79 | 0.82 | 96 | AMP |
| 2 | 1063 | 0.76 | 0.79 | 56 | empty |
| 3 | 161 | 0.65 | 0.85 | 32 | empty |
| 4 | 85 | 0.42 | 0.78 | 19 | empty |
| 5 | 68 | 0.29 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–P · 507 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–T · 505 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- T–D · 343 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- A–D · 172 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–T · 162 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6BKF · Lysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate in open… · the same entry in another collection · chain A against A, TM-score 1.00
- P49917 · AlphaFold monomer V2.0 prediction for DNA ligase 4 (P49917) · a predicted model of the same protein · chain A against A, TM-score 0.77
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 P49917
- Elsewhere: RCSB PDB 6BKF · PDBe 6BKF · UniProt P49917
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