MolNFT v1 · #99753 · protein
Crystal structure of a hd-gyp domain (a cyclic-di-gmp phosphodiesterase) containing a tri-nuclear metal centre
4MCW · Metal dependent phosphohydrolase: “Crystal structure of a hd-gyp domain (a cyclic-di-gmp phosphodiesterase) containing a tri-nuclear metal centre”. X-ray diffraction, 1 ligand (FE), 8 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 4MCW
- Type
- protein
- Length
- 724 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metal dependent phosphohydrolase
- EC
- 3.1.4.1
- UniProt
- C0QQ26
- Ligands
- FE
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metal dependent phosphohydrolase (EC 3.1.4.1) | protein | 361 | 58% helix, 12% strand | C0QQ26 |
| B | Metal dependent phosphohydrolase (EC 3.1.4.1) | protein | 363 | 57% helix, 12% strand | C0QQ26 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 6 copies · chains A, B
- SIN · Succinic acid · additive · 6 copies · chains A, B
- IMD · Imidazole · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.73 | 0.82 | 62 | empty |
| 2 | 336 | 0.67 | 0.81 | 36 | empty |
| 3 | 539 | 0.67 | 0.77 | 48 | empty |
| 4 | 377 | 0.65 | 0.79 | 41 | empty |
| 5 | 399 | 0.56 | 0.74 | 32 | FE, SIN |
Interfaces
1 interface between chains.
- A–B · 3016 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 4MCW · 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 4MCW · PDBe 4MCW · UniProt C0QQ26
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