Research workbench
Crystal structure of NEC3PO in complex with ssdna.
Analyse Crystal structure of NEC3PO in complex with ssdna. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JRE
- Type
- protein + DNA
- Length
- 1,488 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NEQ131; Ssdna
- UniProt
- Q74ML9
- Ligands
- ADE, ADZ
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | NEQ131 | protein | 186 | 85% helix, 0% strand | Q74ML9 |
| B, F | NEQ131 | protein | 184 | 85% helix, 0% strand | Q74ML9 |
| C, G | NEQ131 | protein | 186 | 85% helix, 0% strand | Q74ML9 |
| D, H | NEQ131 | protein | 185 | 85% helix, 0% strand | Q74ML9 |
| I, J | Ssdna | dna | 3 | — | — |
Ligands and binding sites
- ADE · Adenine · ligand · 5 copies · chains A, B, D, G, H, C
- ADZ · 9-methyl-9H-purin-6-amine · ligand · 3 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.78 | 0.81 | 83 | empty |
| 2 | 580 | 0.73 | 0.81 | 61 | ADE |
| 3 | 265 | 0.65 | 0.82 | 44 | empty |
| 4 | 229 | 0.63 | 0.82 | 30 | empty |
| 5 | 317 | 0.63 | 0.79 | 39 | empty |
Interfaces
27 interfaces between chains.
- A–B · 2101 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 2086 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2065 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2064 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 925 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5JRE · Crystal structure of NeC3PO in complex with ssDNA. · the same entry in another collection · chain A against A, 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 Q74ML9
- Elsewhere: RCSB PDB 5JRE · PDBe 5JRE · UniProt Q74ML9
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