Research workbench
Structure of mcrbc without DNA binding domains (one half of the full complex)
Analyse Structure of mcrbc without DNA binding domains (one half of the full complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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