MolNFT v1 · #160126 · protein + DNA
DNA N6-adenine methyltransferase ccrm in complex with double-stranded DNA oligonucleotide containing its recognition sequence gaatc
6PBD · Modification methylase ccrmi: “DNA N6-adenine methyltransferase ccrm in complex with double-stranded DNA oligonucleotide containing its…”. X-ray diffraction, 1 ligand (SFG), 9 pockets (best druggability 0.73). MolNFT v1 #160126 on…
- PDB
- 6PBD
- Type
- protein + DNA
- Length
- 719 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Modification methylase ccrmi; DNA (5'- D(*CP*GP*AP*TP*TP*CP*AP*AP*TP*GP*AP*AP*TP*CP*CP*CP*…
- EC
- 2.1.1.72
- UniProt
- P0CAW2
- Ligands
- SFG
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Modification methylase ccrmi (EC 2.1.1.72) | protein | 350 | 28% helix, 23% strand | P0CAW2 |
| B | Modification methylase ccrmi (EC 2.1.1.72) | protein | 331 | 34% helix, 23% strand | P0CAW2 |
| X | DNA (5'- D(*CP*GP*AP*TP*TP*CP*AP*AP*TP*GP*AP*AP*TP*CP*CP*CP*AP*AP*G)-3') | dna | 19 | — | — |
| Y | DNA (5'- D(*GP*CP*TP*TP*GP*GP*GP*AP*TP*TP*CP*AP*TP*TP*GP*AP*AP*TP*C)-3') | dna | 19 | — | — |
Ligands and binding sites
- SFG · Sinefungin · ligand · 2 copies · chains A, X, B
- EDO · 1,2-ethanediol · additive · chains A, B, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.73 | 0.91 | 33 | SFG |
| 2 | 575 | 0.70 | 0.79 | 77 | empty |
| 3 | 203 | 0.62 | 0.82 | 32 | SFG |
| 4 | 288 | 0.58 | 0.78 | 39 | EDO |
| 5 | 212 | 0.54 | 0.79 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3241 Ų buried · 52 hydrogen bonds · protein-protein
- A–X · 1190 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–Y · 701 Ų buried · 10 hydrogen bonds · protein-nucleic
- X–Y · 648 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–Y · 507 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 6PBD · DNA N6-Adenine Methyltransferase CcrM In Complex with Double-Stranded DNA Oligonucleotide… · the same entry in another collection · chain B against B, TM-score 1.00
- P0CAW2 · AlphaFold monomer V2.0 prediction for modification methylase ccrmi (P0CAW2) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P0CAW2
- Elsewhere: RCSB PDB 6PBD · PDBe 6PBD · UniProt P0CAW2
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