MolNFT v1 · #15393 · protein + DNA
Crystal structure of I-crei bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence)
1N3F · 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*GP*A)- 3': “Crystal structure of I-crei bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA…”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability…
- PDB
- 1N3F
- Type
- protein + DNA
- Length
- 692 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*GP*A)- 3'…
- EC
- 3.1.-.-
- UniProt
- P05725
- Ligands
- CA
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E, I, K | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*GP*A)- 3' | dna | 14 | — | — |
| D, F, J, L | 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G-3') | dna | 10 | — | — |
| A, B, G, H | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 149 | 55% helix, 21% strand | P05725 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains C, D, E, F, A, B, I, J, K, L, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.77 | 0.95 | 33 | empty |
| 2 | 134 | 0.77 | 0.95 | 33 | empty |
| 3 | 117 | 0.76 | 0.95 | 31 | empty |
| 4 | 63 | 0.68 | 0.96 | 22 | empty |
| 5 | 56 | 0.40 | 0.81 | 16 | empty |
Interfaces
32 interfaces between chains.
- A–B · 1023 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1019 Ų buried · 18 hydrogen bonds · protein-protein
- I–G · 868 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–B · 856 Ų buried · 17 hydrogen bonds · protein-nucleic
- K–H · 845 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 1N3F · Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right… · the same entry in another collection · chain H against H, 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 P05725
- Elsewhere: RCSB PDB 1N3F · PDBe 1N3F · UniProt P05725
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