MolNFT v1 · #22091 · protein + DNA
The structure of K92A ecorv bound to cognate DNA and MG2+
1SUZ · 5'-D(*C*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3': “The structure of K92A ecorv bound to cognate DNA and MG2+”. X-ray diffraction, 2 ligands (MG, NA), 3 pockets (best druggability 0.82). MolNFT v1 #22091 on GenesisL1: 3D structure, binding…
- PDB
- 1SUZ
- Type
- protein + DNA
- Length
- 500 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*C*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'; Type II restriction enzyme ecorv
- EC
- 3.1.21.4
- UniProt
- P04390
- Ligands
- MG, NA
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*C*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3' | dna | 10 | — | — |
| D | 5'-D(*C*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3' | dna | 10 | — | — |
| A | Type II restriction enzyme ecorv (EC 3.1.21.4) | protein | 243 | 35% helix, 25% strand | P04390 |
| B | Type II restriction enzyme ecorv (EC 3.1.21.4) | protein | 237 | 33% helix, 26% strand | P04390 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, A, D, B
- NA · Sodium ion · metal · 2 copies · chains C, A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.82 | 0.88 | 79 | empty |
| 2 | 427 | 0.62 | 0.77 | 53 | empty |
| 3 | 235 | 0.56 | 0.78 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1923 Ų buried · 25 hydrogen bonds · protein-protein
- C–A · 756 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–B · 742 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–A · 434 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 420 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Compared structures
- 1SUZ · The structure of K92A EcoRV bound to cognate DNA and Mg2+ · the same entry in another collection · chain C against C, TM-score 1.00
- P04390 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme ecorv (P04390) · a predicted model of the same protein · 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 P04390
- Elsewhere: RCSB PDB 1SUZ · PDBe 1SUZ · UniProt P04390
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