MolNFT v1 · #102292 · protein
Crystal structure of cytosolic nucleotidase II (LPG0095) in complex with gmp from legionella pneumophila, northeast structural genomics consortium target LGR1
4OHF · Cytosolic imp-gmp specific 5'-nucleotidase: “Crystal structure of cytosolic nucleotidase II (LPG0095) in complex with gmp from legionella pneumophila…”. X-ray diffraction, 3 ligands (5GP, MG, PO4), 20 pockets (best druggability…
- PDB
- 4OHF
- Type
- protein
- Length
- 1,807 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosolic imp-gmp specific 5'-nucleotidase
- UniProt
- Q5ZZB6
- Ligands
- 5GP, MG, PO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic imp-gmp specific 5'-nucleotidase | protein | 455 | 45% helix, 17% strand | Q5ZZB6 |
| B | Cytosolic imp-gmp specific 5'-nucleotidase | protein | 458 | 47% helix, 17% strand | Q5ZZB6 |
| C | Cytosolic imp-gmp specific 5'-nucleotidase | protein | 438 | 43% helix, 18% strand | Q5ZZB6 |
| D | Cytosolic imp-gmp specific 5'-nucleotidase | protein | 456 | 47% helix, 17% strand | Q5ZZB6 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains B, C, D
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.87 | 0.89 | 100 | PO4 |
| 2 | 784 | 0.82 | 0.85 | 80 | PO4 |
| 3 | 688 | 0.76 | 0.81 | 69 | PO4 |
| 4 | 286 | 0.68 | 0.83 | 40 | PO4, MG |
| 5 | 347 | 0.68 | 0.82 | 34 | PO4 |
Interfaces
4 interfaces between chains.
- A–B · 3086 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2824 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 250 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 61 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4OHF · Crystal structure of cytosolic nucleotidase II (LPG0095) in complex with GMP from… · the same entry in another collection · chain B against B, 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 Q5ZZB6
- Elsewhere: RCSB PDB 4OHF · PDBe 4OHF · UniProt Q5ZZB6
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