MolNFT v1 · #34151 · protein + DNA
Crystal structure of the aa complex of the N-terminal domain of pria
2D7G · Primosomal protein N': “Crystal structure of the aa complex of the N-terminal domain of pria”. X-ray diffraction, 5 pockets (best druggability 0.72). MolNFT v1 #34151 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2D7G
- Type
- protein + DNA
- Length
- 417 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Primosomal protein N'; DNA (5'-D(P*AP*A)-3')
- EC
- 3.6.4.-
- UniProt
- P17888
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Primosomal protein N' (EC 3.6.4.-) | protein | 104 | 25% helix, 28% strand | P17888 |
| B | Primosomal protein N' (EC 3.6.4.-) | protein | 104 | 24% helix, 26% strand | P17888 |
| C | Primosomal protein N' (EC 3.6.4.-) | protein | 105 | 24% helix, 28% strand | P17888 |
| D | Primosomal protein N' (EC 3.6.4.-) | protein | 100 | 24% helix, 29% strand | P17888 |
| E, F, G, H | DNA (5'-D(P*AP*A)-3') | dna | 1 | — | — |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.72 | 0.81 | 50 | empty |
| 2 | 526 | 0.70 | 0.79 | 55 | empty |
| 3 | 220 | 0.64 | 0.83 | 35 | empty |
| 4 | 86 | 0.39 | 0.77 | 20 | empty |
| 5 | 66 | 0.34 | 0.77 | 15 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2113 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2024 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 753 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 293 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–F · 285 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 2D7G · Crystal structure of the aa complex of the N-terminal domain of PriA · the same entry in another collection · chain D against D, TM-score 1.00
- P17888 · AlphaFold monomer V2.0 prediction for primosomal protein N' (P17888) · a predicted model of the same protein · chain D against A, TM-score 0.85
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 P17888
- Elsewhere: RCSB PDB 2D7G · PDBe 2D7G · UniProt P17888
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