Research workbench
Crystal structure of gmp reductase from mycobacterium smegmatis in complex with gmp.
Analyse Crystal structure of gmp reductase from mycobacterium smegmatis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R50
- Type
- protein
- Length
- 7,307 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5-monophosphate dehydrogenase GUAB1
- EC
- 1.1.1.-
- UniProt
- I7GA39
- Ligands
- 5GP
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 16 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 473 | 33% helix, 19% strand | I7GA39 |
| B | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 447 | 34% helix, 20% strand | I7GA39 |
| C | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 446 | 34% helix, 22% strand | I7GA39 |
| D | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 468 | 33% helix, 20% strand | I7GA39 |
| E | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 468 | 33% helix, 19% strand | I7GA39 |
| F | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 440 | 33% helix, 20% strand | I7GA39 |
| G | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 424 | 35% helix, 18% strand | I7GA39 |
| H | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 468 | 33% helix, 21% strand | I7GA39 |
| I | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 466 | 35% helix, 20% strand | I7GA39 |
| J | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 440 | 34% helix, 18% strand | I7GA39 |
| K | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 450 | 32% helix, 21% strand | I7GA39 |
| L | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 465 | 33% helix, 19% strand | I7GA39 |
| M | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 471 | 35% helix, 20% strand | I7GA39 |
| N | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 461 | 33% helix, 20% strand | I7GA39 |
| O | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 455 | 34% helix, 20% strand | I7GA39 |
| P | Inosine-5-monophosphate dehydrogenase GUAB1 (EC 1.1.1.-) | protein | 465 | 33% helix, 20% strand | I7GA39 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.87 | 0.89 | 105 | empty |
| 2 | 756 | 0.84 | 0.88 | 103 | 5GP |
| 3 | 527 | 0.84 | 0.90 | 76 | 5GP |
| 4 | 551 | 0.84 | 0.90 | 85 | 5GP |
| 5 | 372 | 0.84 | 0.93 | 58 | 5GP |
Interfaces
41 interfaces between chains.
- M–N · 2262 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 2241 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 2228 Ų buried · 27 hydrogen bonds · protein-protein
- N–O · 2208 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 2196 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 7R50 · Crystal structure of GMP reductase from mycobacterium smegmatis in complex with GMP. · 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 I7GA39
- Elsewhere: RCSB PDB 7R50 · PDBe 7R50 · UniProt I7GA39
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