Research workbench
Crystal structure of cytosolic nucleotidase II (LPG0095) in complex with gmp from legionella pneumophila, northeast structural genomics consortium target LGR1
Analyse Crystal structure of cytosolic nucleotidase II (LPG0095) in complex with gmp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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