Research workbench
Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate
Analyse Crystal structure of the ligase from bacteriophage T4 complexed with DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DT1
- Type
- protein + DNA
- Length
- 1,007 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase; DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(DOC))-3'); DNA…
- EC
- 6.5.1.1
- UniProt
- P00970
- Ligands
- AMP, MG, CL
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase (EC 6.5.1.1) | protein | 464 | 36% helix, 24% strand | P00970 |
| E | DNA ligase (EC 6.5.1.1) | protein | 459 | 36% helix, 24% strand | P00970 |
| B, F | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(DOC))-3') | dna | 11 | — | — |
| C, G | DNA (5'-D((AMP)*GP*TP*CP*GP*GP*AP*CP*TP*GP*AP*)-3') | dna | 10 | — | — |
| D, H | DNA (5'- D(*TP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 21 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains E, F, G, A, C
- MG · Magnesium ion · metal · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, E
- GOL · Glycerol · additive · 12 copies · chains A, D, C, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 5 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.81 | 0.82 | 61 | AMP |
| 2 | 1077 | 0.80 | 0.82 | 74 | GOL, DTT, CL, MG, AMP |
| 3 | 845 | 0.73 | 0.77 | 70 | CL |
| 4 | 356 | 0.68 | 0.82 | 37 | 1PE |
| 5 | 245 | 0.65 | 0.83 | 30 | empty |
Interfaces
14 interfaces between chains.
- E–H · 1356 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–D · 1345 Ų buried · 31 hydrogen bonds · protein-nucleic
- E–G · 647 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 640 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–E · 629 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 2 modified (covalent ligand, nucleotide modification).
Compared structures
- 6DT1 · Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate · 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 P00970
- Elsewhere: RCSB PDB 6DT1 · PDBe 6DT1 · UniProt P00970
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