Research workbench
Crystal structure of 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase from neisseria gonorrhoeae
Analyse Crystal structure of 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UM0
- Type
- protein
- Length
- 918 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
- EC
- 5.4.2.11
- UniProt
- B4RIY7
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.11) | protein | 230 | 44% helix, 15% strand | B4RIY7 |
| D | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (EC 5.4.2.11) | protein | 228 | 45% helix, 15% strand | B4RIY7 |
Ligands and binding sites
- TLA · L(+)-tartaric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.73 | 0.81 | 55 | empty |
| 2 | 398 | 0.68 | 0.80 | 51 | empty |
| 3 | 178 | 0.60 | 0.83 | 27 | TLA |
| 4 | 348 | 0.56 | 0.75 | 39 | empty |
| 5 | 350 | 0.55 | 0.74 | 44 | empty |
Interfaces
4 interfaces between chains.
- C–D · 941 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 921 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 642 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 626 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5UM0 · Crystal structure of 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase from… · the same entry in another collection · chain A against A, TM-score 1.00
- B4RIY7 · AlphaFold monomer V2.0 prediction for 2,3-bisphosphoglycerate- dependent phosphoglycerate… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 B4RIY7
- Elsewhere: RCSB PDB 5UM0 · PDBe 5UM0 · UniProt B4RIY7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.