MolNFT v1 · #34742 · protein
Crystal structure of the gmp synthase from pyrococcus horikoshii OT3
2DPL · Gmp synthase [glutamine-hydrolyzing] subunit B: “Crystal structure of the gmp synthase from pyrococcus horikoshii OT3”. X-ray diffraction, 5 pockets (best druggability 0.58). MolNFT v1 #34742 on GenesisL1: 3D structure, binding…
- PDB
- 2DPL
- Type
- protein
- Length
- 565 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gmp synthase [glutamine-hydrolyzing] subunit B
- EC
- 6.3.5.2
- UniProt
- O59072
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gmp synthase [glutamine-hydrolyzing] subunit B (EC 6.3.5.2) | protein | 287 | 45% helix, 21% strand | O59072 |
| B | Gmp synthase [glutamine-hydrolyzing] subunit B (EC 6.3.5.2) | protein | 278 | 45% helix, 19% strand | O59072 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.58 | 0.75 | 50 | empty |
| 2 | 333 | 0.58 | 0.76 | 29 | empty |
| 3 | 243 | 0.57 | 0.79 | 25 | empty |
| 4 | 306 | 0.55 | 0.75 | 40 | empty |
| 5 | 164 | 0.40 | 0.73 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1581 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2DPL · Crystal Structure of the GMP synthase from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00
- O59072 · AlphaFold monomer V2.0 prediction for gmp synthase [glutamine- hydrolyzing] subunit B… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O59072
- Elsewhere: RCSB PDB 2DPL · PDBe 2DPL · UniProt O59072
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