MolNFT v1 · #162347 · protein + DNA
N-terminal domain of modification dependent ecokmcra restriction endonuclease (neco) in complex with C5MCGG target sequence
6R64 · 5-methylcytosine-specific restriction enzyme a: “N-terminal domain of modification dependent ecokmcra restriction endonuclease (neco) in complex with C5MCGG…”. X-ray diffraction, 3 pockets (best druggability 0.63). MolNFT v1 #162347…
- PDB
- 6R64
- Type
- protein + DNA
- Length
- 330 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methylcytosine-specific restriction enzyme a; DNA…
- EC
- 3.1.21.-
- UniProt
- P24200
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5-methylcytosine-specific restriction enzyme a (EC 3.1.21.-) | protein | 145 | 32% helix, 25% strand | P24200 |
| C, E | DNA (5'-D(*TP*CP*AP*CP*(5CM)P*GP*GP*TP*TP*C)-3') | dna | 10 | — | — |
| D, F | DNA (5'-D(*GP*AP*AP*CP*(5CM)P*GP*GP*TP*GP*A)-3') | dna | 10 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.63 | 0.76 | 50 | empty |
| 2 | 88 | 0.31 | 0.72 | 29 | empty |
| 3 | 58 | 0.26 | 0.74 | 12 | empty |
Interfaces
9 interfaces between chains.
- B–E · 567 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 562 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–B · 507 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 483 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 464 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6R64 · N-terminal domain of modification dependent EcoKMcrA restriction endonuclease (NEco) in… · the same entry in another collection · chain C against C, TM-score 1.00
- P24200 · AlphaFold monomer V2.0 prediction for 5-methylcytosine-specific restriction enzyme a… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P24200
- Elsewhere: RCSB PDB 6R64 · PDBe 6R64 · UniProt P24200
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