MolNFT v1 · #142068 · protein
Acetylation of lysine 100 of phosphoglycerate mutase 1 complexed with KH_OL
5ZS8: “Acetylation of lysine 100 of phosphoglycerate mutase 1 complexed with KH_OL”. X-ray diffraction, 2 ligands (9JF, CL), 6 pockets (best druggability 0.64). MolNFT v1 #142068 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ZS8
- Type
- protein
- Length
- 473 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate mutase 1
- EC
- 5.4.2.11, 5.4.2.4
- UniProt
- P18669
- Ligands
- 9JF, CL
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Phosphoglycerate mutase 1 (EC 5.4.2.11, 5.4.2.4) | protein | 233 | 45% helix, 12% strand | P18669 |
| C | Phosphoglycerate mutase 1 (EC 5.4.2.11, 5.4.2.4) | protein | 240 | 45% helix, 14% strand | P18669 |
Ligands and binding sites
- 9JF · N-(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)-2-hydroxybenzene-1-sulfonamide · ligand · chains C
- CL · Chloride ion · ion · chains B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.64 | 0.78 | 33 | MES, 9JF |
| 2 | 217 | 0.56 | 0.79 | 30 | empty |
| 3 | 166 | 0.45 | 0.75 | 21 | empty |
| 4 | 159 | 0.44 | 0.75 | 23 | empty |
| 5 | 100 | 0.40 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- B–C · 1100 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation, phosphorylation).
Compared structures
- 5ZS8 · Acetylation of lysine 100 of Phosphoglycerate mutase 1 complexed with KH_ol · the same entry in another collection · chain B against B, TM-score 1.00
- P18669 · AlphaFold monomer V2.0 prediction for phosphoglycerate mutase 1 (P18669) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P18669
- Elsewhere: RCSB PDB 5ZS8 · PDBe 5ZS8 · UniProt P18669
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