MolNFT v1 · #146803 · protein + DNA
Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate
6DT1 · DNA ligase: “Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate”. X-ray diffraction, 3 ligands (AMP, MG, CL), 12 pockets (best druggability 0.81). MolNFT v1 #146803 on GenesisL1: 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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