Research workbench
Structure of T4 RNA ligase 2 with nicked 5'-adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick
Analyse Structure of T4 RNA ligase 2 with nicked 5'-adenylated nucleic acid duplex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HVS
- Type
- protein + DNA
- Length
- 734 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP *CP*AP*AP*TP*TP*G)-3'…
- UniProt
- P32277
- Ligands
- AMP
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, F | 5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP *CP*AP*AP*TP*TP*G)-3' | dna | 24 | — | — |
| D, G | 5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3' | dna | 12 | — | — |
| E, H | 5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3' | dna | 12 | — | — |
| A | T4 RNA ligase 2 | protein | 319 | 35% helix, 21% strand | P32277 |
| B | T4 RNA ligase 2 | protein | 319 | 36% helix, 22% strand | P32277 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains E, A, H, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains C, D, F, G, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.74 | 0.77 | 75 | AMP |
| 2 | 603 | 0.68 | 0.78 | 53 | AMP |
| 3 | 267 | 0.53 | 0.76 | 24 | empty |
| 4 | 265 | 0.52 | 0.76 | 26 | empty |
| 5 | 112 | 0.47 | 0.80 | 13 | empty |
Interfaces
15 interfaces between chains.
- C–D · 554 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- F–G · 549 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- C–E · 536 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- F–H · 525 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- F–B · 338 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nucleotide modification).
Compared structures
- 2HVS · Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a… · the same entry in another collection · chain F against F, 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 P32277
- Elsewhere: RCSB PDB 2HVS · PDBe 2HVS · UniProt P32277
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