Research workbench
Crystal structure of PA4781 hd-gyp domain from pseudomonas aeruginosa at 2.2A resolution showing a bi-metallic ni ion center
Analyse Crystal structure of PA4781 hd-gyp domain from pseudomonas aeruginosa at 2.2A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R8Z
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic di-gmp phosphodiesterase
- EC
- 3.1.4.1
- UniProt
- Q9HV27
- Ligands
- NI, CL
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic di-gmp phosphodiesterase (EC 3.1.4.1) | protein | 218 | 64% helix, 2% strand | Q9HV27 |
| B | Cyclic di-gmp phosphodiesterase (EC 3.1.4.1) | protein | 217 | 67% helix, 1% strand | Q9HV27 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.62 | 0.76 | 41 | empty |
| 2 | 415 | 0.61 | 0.76 | 37 | empty |
| 3 | 166 | 0.46 | 0.76 | 32 | empty |
| 4 | 140 | 0.40 | 0.74 | 22 | empty |
| 5 | 61 | 0.36 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1550 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4R8Z · Crystal Structure of PA4781 HD-GYP domain from Pseudomonas aeruginosa at 2.2A resolution… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HV27 · AlphaFold monomer V2.0 prediction for cyclic di-gmp phosphodiesterase PA4781 (Q9HV27) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q9HV27
- Elsewhere: RCSB PDB 4R8Z · PDBe 4R8Z · UniProt Q9HV27
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