Research workbench
DNA binding and cleavage by the giy-yig endonuclease R.ECO29KI inactive variant Y49F
Analyse DNA binding and cleavage by the giy-yig endonuclease R.ECO29KI inactive variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NIC
- Type
- protein + DNA
- Length
- 1,850 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ECO29KIR; DNA (5'- D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)…
- EC
- 3.1.21.4
- UniProt
- Q46944
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ECO29KIR (EC 3.1.21.4) | protein | 210 | 42% helix, 11% strand | Q46944 |
| C, D, F, G, H | ECO29KIR (EC 3.1.21.4) | protein | 209 | 42% helix, 12% strand | Q46944 |
| E | ECO29KIR (EC 3.1.21.4) | protein | 209 | 39% helix, 12% strand | Q46944 |
| M, I, K, O | DNA (5'- D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C) -3') | dna | 22 | — | — |
| N, J, L, P | DNA (5'- D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G) -3') | dna | 22 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 11 copies · chains A, B, D, E, F, O, G, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.86 | 0.87 | 75 | empty |
| 2 | 1066 | 0.83 | 0.85 | 75 | empty |
| 3 | 597 | 0.82 | 0.87 | 70 | empty |
| 4 | 419 | 0.81 | 0.89 | 49 | empty |
| 5 | 880 | 0.77 | 0.80 | 63 | empty |
Interfaces
31 interfaces between chains.
- A–H · 2971 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 2935 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 2855 Ų buried · 36 hydrogen bonds · protein-protein
- C–G · 2775 Ų buried · 33 hydrogen bonds · protein-protein
- O–P · 1075 Ų buried · 132 hydrogen bonds · nucleic-nucleic
Compared structures
- 3NIC · DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F · 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 Q46944
- Elsewhere: RCSB PDB 3NIC · PDBe 3NIC · UniProt Q46944
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