MolNFT v1 · #151823 · protein
Structure of mcrbc without DNA binding domains (one half of the full complex)
6HZ4 · 5-methylcytosine-specific restriction enzyme B: “Structure of mcrbc without DNA binding domains (one half of the full complex)”. Electron microscopy, 3 ligands (GNP, GDP, MG), 20 pockets (best druggability 0.87). MolNFT v1 #151823…
- PDB
- 6HZ4
- Type
- protein
- Length
- 2,212 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methylcytosine-specific restriction enzyme B; Protein mcrc
- EC
- 3.1.21.-
- UniProt
- P15005, P15006
- Ligands
- GNP, GDP, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 290 | 48% helix, 13% strand | P15005 |
| D | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 284 | 42% helix, 12% strand | P15005 |
| E, F | 5-methylcytosine-specific restriction enzyme B (EC 3.1.21.-) | protein | 285 | 45% helix, 13% strand | P15005 |
| M | Protein mcrc | protein | 336 | 40% helix, 19% strand | P15006 |
| N | Protein mcrc | protein | 152 | 32% helix, 26% strand | P15006 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains D, E, F, A
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.87 | 0.88 | 120 | GDP |
| 2 | 645 | 0.84 | 0.89 | 104 | empty |
| 3 | 1005 | 0.83 | 0.84 | 97 | empty |
| 4 | 1139 | 0.80 | 0.81 | 98 | GDP |
| 5 | 1010 | 0.80 | 0.81 | 93 | GDP |
Interfaces
14 interfaces between chains.
- A–B · 2163 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 2079 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1892 Ų buried · 12 hydrogen bonds · protein-protein
- M–N · 1537 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1206 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6HZ4 · Structure of McrBC without DNA binding domains (one half of the full complex) · the same entry in another collection · chain F against F, 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 A against A, TM-score 0.98
- P15006 · AlphaFold monomer V2.0 prediction for protein mcrc (P15006) · a predicted model of the same protein · chain M against A, TM-score 0.93
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
- Every structure of UniProt P15006
- Elsewhere: RCSB PDB 6HZ4 · PDBe 6HZ4 · UniProt P15005 · UniProt P15006
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