MolNFT v1 · #99794 · protein
Crystal structure of a hd-gyp domain (a cyclic-di-gmp phosphodiesterase) containing a tri-nuclear metal centre
4ME4 · Metal dependent phosphohydrolase: “Crystal structure of a hd-gyp domain (a cyclic-di-gmp phosphodiesterase) containing a tri-nuclear metal centre”. X-ray diffraction, 2 ligands (5GP, FE), 9 pockets (best druggability 0.75). MolNFT…
- PDB
- 4ME4
- Type
- protein
- Length
- 724 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metal dependent phosphohydrolase
- UniProt
- C0QQ26
- Ligands
- 5GP, FE
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metal dependent phosphohydrolase | protein | 361 | 58% helix, 12% strand | C0QQ26 |
| B | Metal dependent phosphohydrolase | protein | 363 | 57% helix, 12% strand | C0QQ26 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · chains B
- FE · Fe (III) ion · metal · 6 copies · chains A, B
- SIN · Succinic acid · additive · 5 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
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 | 342 | 0.75 | 0.86 | 46 | empty |
| 2 | 363 | 0.68 | 0.81 | 37 | empty |
| 3 | 343 | 0.67 | 0.81 | 36 | empty |
| 4 | 542 | 0.67 | 0.77 | 46 | empty |
| 5 | 490 | 0.61 | 0.75 | 35 | FE, 5GP, SIN |
Interfaces
1 interface between chains.
- A–B · 3084 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 4ME4 · Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a… · the same entry in another collection · chain A 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 C0QQ26
- Elsewhere: RCSB PDB 4ME4 · PDBe 4ME4 · UniProt C0QQ26
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