MolNFT v1 · #46632 · protein + DNA
Restriction endonuclease mvai-cognate DNA substrate complex
2OAA · 5'-D(*GP*GP*TP*AP*CP*CP*TP*GP*GP*AP*T)-3': “Restriction endonuclease mvai-cognate DNA substrate complex”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.69). MolNFT v1 #46632 on GenesisL1: 3D structure, binding…
- PDB
- 2OAA
- Type
- protein + DNA
- Length
- 538 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*TP*AP*CP*CP*TP*GP*GP*AP*T)-3'; 5'-D(*CP*AP*TP*CP*CP*AP*GP*GP*TP*AP*C)-3'…
- UniProt
- Q8RNV5
- Ligands
- CA
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*GP*GP*TP*AP*CP*CP*TP*GP*GP*AP*T)-3' | dna | 10 | — | — |
| D, F | 5'-D(*CP*AP*TP*CP*CP*AP*GP*GP*TP*AP*C)-3' | dna | 11 | — | — |
| E | 5'-D(*GP*GP*TP*AP*CP*CP*TP*GP*GP*AP*T)-3' | dna | 11 | — | — |
| A | R.MVAI | protein | 247 | 24% helix, 38% strand | Q8RNV5 |
| B | R.MVAI | protein | 248 | 24% helix, 37% strand | Q8RNV5 |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains C, A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.69 | 0.80 | 49 | empty |
| 2 | 186 | 0.52 | 0.78 | 31 | CA |
| 3 | 59 | 0.31 | 0.76 | 19 | empty |
| 4 | 50 | 0.22 | 0.71 | 9 | empty |
Interfaces
11 interfaces between chains.
- E–B · 1238 Ų buried · 30 hydrogen bonds · protein-nucleic
- C–A · 1211 Ų buried · 31 hydrogen bonds · protein-nucleic
- D–A · 1076 Ų buried · 26 hydrogen bonds · protein-nucleic
- F–B · 1048 Ų buried · 26 hydrogen bonds · protein-nucleic
- E–F · 509 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Compared structures
- 2OAA · Restriction endonuclease MvaI-cognate DNA substrate complex · the same entry in another collection · chain C against C, 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 Q8RNV5
- Elsewhere: RCSB PDB 2OAA · PDBe 2OAA · UniProt Q8RNV5
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