Research workbench
Human ligiv catalytic domain with bound DNA-adenylate intermediate in closed conformation
Analyse Human ligiv catalytic domain with bound DNA-adenylate intermediate in closed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BKG
- Type
- protein + DNA
- Length
- 636 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, NA, CL
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase 4 (EC 6.5.1.1) | protein | 600 | 36% 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*(AMP)P*GP*TP*CP*GP*GP*AP*C)-3') | dna | 7 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A, P, D
- NA · Sodium ion · metal · chains A, D
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.82 | 0.83 | 71 | empty |
| 2 | 139 | 0.78 | 0.96 | 20 | AMP |
| 3 | 291 | 0.73 | 0.86 | 35 | empty |
| 4 | 745 | 0.71 | 0.78 | 53 | empty |
| 5 | 116 | 0.43 | 0.77 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–T · 1011 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 671 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–T · 500 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- A–D · 480 Ų buried · 10 hydrogen bonds · protein-nucleic
- T–D · 353 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6BKG · Human LigIV catalytic domain with bound DNA-adenylate intermediate in closed conformation · the same entry in another collection · chain P against P, 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 0.99
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 6BKG · PDBe 6BKG · UniProt P49917
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