MolNFT v1 · #145598 · protein + DNA
Structure of human DNA polymerase kappa with DNA
6CST: “Structure of human DNA polymerase kappa with DNA”. X-ray diffraction, 5 ligands (DZ4, MG, K), 15 pockets (best druggability 0.87). MolNFT v1 #145598 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6CST
- Type
- protein + DNA
- Length
- 932 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase kappa; DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UBT6
- Ligands
- DZ4, MG, K, CL, IOD
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase kappa (EC 2.7.7.7) | protein | 446 | 49% helix, 19% strand | Q9UBT6 |
| B | DNA polymerase kappa (EC 2.7.7.7) | protein | 442 | 50% helix, 19% strand | Q9UBT6 |
| C, P | DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3') | dna | 9 | — | — |
| D, T | DNA (5'-D(P*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3') | dna | 13 | — | — |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · 2 copies · chains A, C, D, B, P, T
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, P
- K · Potassium ion · metal · 4 copies · chains A, B, D
- CL · Chloride ion · ion · 9 copies · chains A, B, T, D
- IOD · Iodide ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, C, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.87 | 0.88 | 102 | MG, IOD, EDO, DZ4, CL |
| 2 | 622 | 0.82 | 0.87 | 71 | CL |
| 3 | 327 | 0.76 | 0.88 | 36 | MG, DZ4 |
| 4 | 230 | 0.70 | 0.87 | 30 | K |
| 5 | 580 | 0.70 | 0.79 | 47 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1392 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1045 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–T · 1000 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 664 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–P · 643 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
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 Q9UBT6
- Elsewhere: RCSB PDB 6CST · PDBe 6CST · UniProt Q9UBT6
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