MolNFT v1 · #15392 · protein + DNA
Crystal structure of I-crei bound to a palindromic DNA sequence I (palindrome of left side of wildtype DNA target sequence)
1N3E · 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)- 3': “Crystal structure of I-crei bound to a palindromic DNA sequence I (palindrome of left side of wildtype DNA…”. X-ray diffraction, 2 ligands (CA, NA), 11 pockets (best druggability…
- PDB
- 1N3E
- Type
- protein + DNA
- Length
- 700 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)- 3'…
- EC
- 3.1.-.-
- UniProt
- P05725
- Ligands
- CA, NA
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E, I, K | 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)- 3' | dna | 14 | — | — |
| D, F, J, L | 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*CP*G)-3' | dna | 10 | — | — |
| A, B, G, H | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 151 | 54% 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
- NA · Sodium ion · metal · 4 copies · chains A, B, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.66 | 0.92 | 24 | empty |
| 2 | 57 | 0.66 | 0.95 | 19 | empty |
| 3 | 81 | 0.65 | 0.92 | 23 | empty |
| 4 | 68 | 0.64 | 0.92 | 14 | empty |
| 5 | 67 | 0.63 | 0.91 | 14 | empty |
Interfaces
33 interfaces between chains.
- G–H · 994 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 975 Ų buried · 18 hydrogen bonds · protein-protein
- E–A · 800 Ų buried · 13 hydrogen bonds · protein-nucleic
- K–G · 797 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–B · 797 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 1N3E · Crystal structure of I-CreI bound to a palindromic DNA sequence I (palindrome of left… · 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 1N3E · PDBe 1N3E · UniProt P05725
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