MolNFT v1 · #52336 · protein
Human gmp synthetase in complex with xmp
2VXO · Gmp synthase [glutamine-hydrolyzing]: “Human gmp synthetase in complex with xmp”. X-ray diffraction, 2 ligands (XMP, SO4), 13 pockets (best druggability 0.84). MolNFT v1 #52336 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2VXO
- Type
- protein
- Length
- 1,301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gmp synthase [glutamine-hydrolyzing]
- EC
- 6.3.5.2
- UniProt
- P49915
- Ligands
- XMP, SO4
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 643 | 38% helix, 21% strand | P49915 |
| B | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 658 | 37% helix, 21% strand | P49915 |
Ligands and binding sites
- XMP · Xanthosine-5'-monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.84 | 0.88 | 73 | XMP, SO4 |
| 2 | 674 | 0.84 | 0.88 | 64 | XMP, SO4 |
| 3 | 478 | 0.79 | 0.86 | 75 | empty |
| 4 | 251 | 0.74 | 0.88 | 40 | empty |
| 5 | 223 | 0.53 | 0.77 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 3924 Ų buried · 60 hydrogen bonds · protein-protein
Compared structures
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 P49915
- Elsewhere: RCSB PDB 2VXO · PDBe 2VXO · UniProt P49915
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