MolNFT v1 · #149851 · protein + DNA
DNA binding domain of restriction endonuclease mcrbc in complex with 5-hydroxymethylcytosine DNA
6GCD · 5-methylcytosine-specific restriction enzyme B: “DNA binding domain of restriction endonuclease mcrbc in complex with 5-hydroxymethylcytosine DNA”. X-ray diffraction, 3 pockets (best druggability 0.63). MolNFT v1 #149851 on…
- PDB
- 6GCD
- Type
- protein + DNA
- Length
- 336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methylcytosine-specific restriction enzyme B; DNA…
- EC
- 3.1.21.-
- UniProt
- P15005
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 159 | 30% helix, 25% strand | P15005 |
| B | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 153 | 28% helix, 25% strand | P15005 |
| C | DNA (5'-D(*GP*AP*GP*AP*(5HC)P*CP*GP*GP*TP*AP*GP*C)-3') | dna | 12 | — | — |
| D | DNA (5'-D(*GP*CP*TP*AP*(5HC)P*CP*GP*GP*TP*CP*TP*C)-3') | dna | 12 | — | — |
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 | 218 | 0.63 | 0.83 | 24 | empty |
| 2 | 226 | 0.63 | 0.83 | 25 | empty |
| 3 | 538 | 0.59 | 0.74 | 29 | empty |
Interfaces
6 interfaces between chains.
- B–C · 663 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–D · 643 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–D · 525 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- A–C · 333 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–D · 298 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (artifact, nucleotide modification).
Compared structures
- 6GCD · DNA binding domain of restriction endonuclease McrBC in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P15005 · AlphaFold monomer V2.0 prediction for 5-methylcytosine-specific restriction enzyme B… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P15005
- Elsewhere: RCSB PDB 6GCD · PDBe 6GCD · UniProt P15005
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