MolNFT v1 · #32989 · protein
Crystal structure of human guanosine monophosphate reductase 2 GMPR2 in complex with imp and NADPH
2C6Q · Gmp reductase 2: “Crystal structure of human guanosine monophosphate reductase 2 GMPR2 in complex with imp and NADPH”. X-ray diffraction, 2 ligands (IMP, NDP), 20 pockets (best druggability 0.82). MolNFT v1 #32989 on GenesisL1: 3D…
- PDB
- 2C6Q
- Type
- protein
- Length
- 2,618 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gmp reductase 2
- EC
- 1.7.1.7
- UniProt
- Q9P2T1
- Ligands
- IMP, NDP
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, H | Gmp reductase 2 (EC 1.7.1.7) | protein | 328 | 38% helix, 23% strand | Q9P2T1 |
| B | Gmp reductase 2 (EC 1.7.1.7) | protein | 329 | 37% helix, 23% strand | Q9P2T1 |
| G | Gmp reductase 2 (EC 1.7.1.7) | protein | 321 | 38% helix, 23% strand | Q9P2T1 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 7 copies · chains A, B, D, C, E, F, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.82 | 0.85 | 63 | IMP, NDP |
| 2 | 741 | 0.82 | 0.85 | 60 | IMP, NDP |
| 3 | 755 | 0.81 | 0.84 | 63 | IMP, NDP |
| 4 | 780 | 0.81 | 0.84 | 62 | IMP, NDP |
| 5 | 978 | 0.81 | 0.82 | 83 | IMP, NDP |
Interfaces
16 interfaces between chains.
- A–B · 1448 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1410 Ų buried · 27 hydrogen bonds · protein-protein
- F–H · 1384 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1369 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1344 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2C6Q · Crystal structure of human guanosine monophosphate reductase 2 GMPR2 in complex with IMP… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9P2T1 · AlphaFold monomer V2.0 prediction for gmp reductase 2 (Q9P2T1) · a predicted model of the same protein · chain B 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 Q9P2T1
- Elsewhere: RCSB PDB 2C6Q · PDBe 2C6Q · UniProt Q9P2T1
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