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Crystal structure of a hd-gyp domain (a cyclic-di-gmp phosphodiesterase) containing a tri-nuclear metal centre
Analyse Crystal structure of a hd-gyp domain (a cyclic-di-gmp phosphodiesterase)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MDZ
- 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
- C2E, FE
- Pockets
- 8 · best druggability 0.74
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 | 56% helix, 11% strand | C0QQ26 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · chains B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- SIN · Succinic acid · additive · 5 copies · chains A, B
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 | 714 | 0.74 | 0.79 | 76 | empty |
| 2 | 341 | 0.66 | 0.80 | 41 | empty |
| 3 | 250 | 0.65 | 0.82 | 31 | empty |
| 4 | 310 | 0.65 | 0.80 | 37 | empty |
| 5 | 523 | 0.61 | 0.74 | 34 | C2E |
Interfaces
1 interface between chains.
- A–B · 3066 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4MDZ · 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 4MDZ · PDBe 4MDZ · UniProt C0QQ26
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