MolNFT v1 · #99302 · protein + DNA
Binary complex of human DNA polymerase mu with DNA
4LZG · DNA-directed DNA/RNA polymerase mu: “Binary complex of human DNA polymerase mu with DNA”. X-ray diffraction, 2 ligands (NA, CL), 2 pockets (best druggability 0.73). MolNFT v1 #99302 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4LZG
- Type
- protein + DNA
- Length
- 342 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed DNA/RNA polymerase mu; Template strand; Upstream primer strand; Downstream…
- EC
- 2.7.7.7
- UniProt
- Q9NP87
- Ligands
- NA, CL
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed DNA/RNA polymerase mu (EC 2.7.7.7) | protein | 325 | 52% helix, 14% strand | Q9NP87 |
| T | Template strand | dna | 9 | — | — |
| P | Upstream primer strand | dna | 4 | — | — |
| D | Downstream primer strand | dna | 4 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, P
- CL · Chloride ion · ion · 2 copies · chains A, D, T
- GOL · Glycerol · additive · chains A, T, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.73 | 0.76 | 59 | GOL, CL |
| 2 | 88 | 0.44 | 0.80 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–T · 718 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–D · 396 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–P · 395 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–P · 226 Ų buried · 15 hydrogen bonds · nucleic-nucleic
- T–D · 196 Ų buried · 15 hydrogen bonds · nucleic-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 Q9NP87
- Elsewhere: RCSB PDB 4LZG · PDBe 4LZG · UniProt Q9NP87
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