Research workbench
Crystal structure of globin domain of the E. COLI dosc - form II (ferrous)
Analyse Crystal structure of globin domain of the E. COLI dosc - form II (ferrous) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZVB
- Type
- protein
- Length
- 598 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate cyclase dosc
- EC
- 2.7.7.65
- UniProt
- P0AA89
- Ligands
- HEM
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Diguanylate cyclase dosc (EC 2.7.7.65) | protein | 150 | 83% helix, 0% strand | P0AA89 |
| B, D | Diguanylate cyclase dosc (EC 2.7.7.65) | protein | 149 | 82% helix, 0% strand | P0AA89 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
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 | 1096 | 0.80 | 0.81 | 88 | empty |
| 2 | 284 | 0.72 | 0.85 | 31 | HEM |
| 3 | 273 | 0.71 | 0.84 | 27 | HEM |
| 4 | 254 | 0.70 | 0.85 | 31 | HEM |
| 5 | 275 | 0.69 | 0.83 | 30 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 1424 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1400 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 211 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 167 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 145 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZVB · Crystal structure of globin domain of the E. coli DosC - form II (ferrous) · the same entry in another collection · chain D against D, TM-score 1.00
- P0AA89 · AlphaFold monomer V2.0 prediction for diguanylate cyclase dosc (P0AA89) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0AA89
- Elsewhere: RCSB PDB 4ZVB · PDBe 4ZVB · UniProt P0AA89
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