Research workbench
Teranry complex of human DNA polymerase IOTA(26-445) inserting dcmpnpp opposite template G in the presence of MN2+
Analyse Teranry complex of human DNA polymerase IOTA(26-445) inserting dcmpnpp opposite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KT3
- Type
- protein + DNA
- Length
- 396 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3'); DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- 0KX, MN
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3') | dna | 10 | — | — |
| P | DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3') | dna | 7 | — | — |
| A | DNA polymerase iota (EC 2.7.7.7) | protein | 379 | 47% helix, 21% strand | Q9UNA4 |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · chains T, P, A
- MN · Manganese (II) ion · metal · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.80 | 0.82 | 81 | 0KX, MN |
| 2 | 359 | 0.69 | 0.82 | 34 | empty |
| 3 | 80 | 0.34 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- T–A · 899 Ų buried · 17 hydrogen bonds · protein-nucleic
- P–A · 511 Ų buried · 11 hydrogen bonds · protein-nucleic
- T–P · 328 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Compared structures
- 5KT3 · Teranry complex of human DNA polymerase iota(26-445) inserting dCMPNPP opposite template… · the same entry in another collection · chain T against T, TM-score 1.00
- Q9UNA4 · AlphaFold monomer V2.0 prediction for DNA polymerase iota (Q9UNA4) · 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 Q9UNA4
- Elsewhere: RCSB PDB 5KT3 · PDBe 5KT3 · UniProt Q9UNA4
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