Research workbench
P. vulgaris higba structure, crystal form 2
Analyse P. vulgaris higba structure, crystal form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MCX
- Type
- protein
- Length
- 553 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antidote protein; Killer protein
- UniProt
- Q7A224, Q7A225
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antidote protein | protein | 93 | 58% helix, 0% strand | Q7A224 |
| B | Killer protein | protein | 93 | 34% helix, 29% strand | Q7A225 |
| C, E | Antidote protein | protein | 92 | 60% helix, 0% strand | Q7A224 |
| D | Killer protein | protein | 92 | 38% helix, 29% strand | Q7A225 |
| F | Killer protein | protein | 91 | 38% helix, 30% strand | Q7A225 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.85 | 0.87 | 108 | empty |
| 2 | 415 | 0.74 | 0.84 | 41 | empty |
| 3 | 81 | 0.35 | 0.75 | 18 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1295 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1036 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1016 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1006 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 428 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4MCX · P. vulgaris HIGBA structure, crystal form 2 · the same entry in another collection · chain F against F, TM-score 1.00
- Q7A225 · AlphaFold monomer V2.0 prediction for endoribonuclease higb (Q7A225) · a predicted model of the same protein · chain F against A, TM-score 0.98
- Q7A224 · AlphaFold monomer V2.0 prediction for antitoxin higa (Q7A224) · 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 Q7A224
- Every structure of UniProt Q7A225
- Elsewhere: RCSB PDB 4MCX · PDBe 4MCX · UniProt Q7A224 · UniProt Q7A225
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