MolNFT v1 · #153919 · protein + DNA
Mutant poliv-DNA incoming nucleotide complex
6JUP · DNA polymerase IV: “Mutant poliv-DNA incoming nucleotide complex”. X-ray diffraction, 2 ligands (0KX, MG), 6 pockets (best druggability 0.82). MolNFT v1 #153919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JUP
- Type
- protein + DNA
- Length
- 750 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'- D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*CP*C)-3')…
- EC
- 2.7.7.7
- UniProt
- W8STT9
- Ligands
- 0KX, MG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 42% helix, 21% strand | W8STT9 |
| G | DNA (5'- D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*CP*C)-3') | dna | 18 | — | — |
| H | DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 14 | — | — |
| B | DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 18 | — | — |
| C | DNA (5'-D(P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 16 | — | — |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · 2 copies · chains F, G, H, A, B, C
- MG · Magnesium ion · metal · 4 copies · chains F, H, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.82 | 0.83 | 85 | 0KX, MG |
| 2 | 1130 | 0.79 | 0.81 | 85 | 0KX, MG |
| 3 | 848 | 0.77 | 0.81 | 57 | empty |
| 4 | 750 | 0.72 | 0.78 | 51 | empty |
| 5 | 102 | 0.38 | 0.75 | 18 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1024 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–G · 904 Ų buried · 17 hydrogen bonds · protein-nucleic
- G–H · 655 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- B–C · 639 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–C · 623 Ų buried · 22 hydrogen bonds · protein-nucleic
Compared structures
- 6JUP · Mutant PolIV-DNA incoming nucleotide complex · 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 W8STT9
- Elsewhere: RCSB PDB 6JUP · PDBe 6JUP · UniProt W8STT9
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