MolNFT v1 · #28625 · protein
Crystal structure of human B type phosphoglycerate mutase
1YJX · Phosphoglycerate mutase 1: “Crystal structure of human B type phosphoglycerate mutase”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.69). MolNFT v1 #28625 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1YJX
- Type
- protein
- Length
- 2,916 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate mutase 1
- EC
- 5.4.2.1, 5.4.2.4, 3.1.3.13
- UniProt
- P18669
- Ligands
- CL
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 9 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, L | Phosphoglycerate mutase 1 (EC 5.4.2.1, 5.4.2.4, 3.1.3.13) | protein | 245 | 44% helix, 13% strand | P18669 |
| B | Phosphoglycerate mutase 1 (EC 5.4.2.1, 5.4.2.4, 3.1.3.13) | protein | 242 | 44% helix, 13% strand | P18669 |
| C | Phosphoglycerate mutase 1 (EC 5.4.2.1, 5.4.2.4, 3.1.3.13) | protein | 243 | 44% helix, 13% strand | P18669 |
| E | Phosphoglycerate mutase 1 (EC 5.4.2.1, 5.4.2.4, 3.1.3.13) | protein | 243 | 44% helix, 14% strand | P18669 |
| F | Phosphoglycerate mutase 1 (EC 5.4.2.1, 5.4.2.4, 3.1.3.13) | protein | 242 | 43% helix, 13% strand | P18669 |
| H | Phosphoglycerate mutase 1 (EC 5.4.2.1, 5.4.2.4, 3.1.3.13) | protein | 241 | 44% helix, 14% strand | P18669 |
| I | Phosphoglycerate mutase 1 (EC 5.4.2.1, 5.4.2.4, 3.1.3.13) | protein | 242 | 44% helix, 13% strand | P18669 |
| J | Phosphoglycerate mutase 1 (EC 5.4.2.1, 5.4.2.4, 3.1.3.13) | protein | 244 | 43% helix, 13% strand | P18669 |
| K | Phosphoglycerate mutase 1 (EC 5.4.2.1, 5.4.2.4, 3.1.3.13) | protein | 239 | 41% helix, 13% strand | P18669 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CIT · Citric acid · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.69 | 0.75 | 88 | CIT |
| 2 | 728 | 0.64 | 0.74 | 89 | empty |
| 3 | 191 | 0.59 | 0.82 | 24 | CIT |
| 4 | 205 | 0.58 | 0.81 | 23 | CIT |
| 5 | 176 | 0.56 | 0.81 | 29 | CIT |
Interfaces
16 interfaces between chains.
- A–B · 1061 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1060 Ų buried · 19 hydrogen bonds · protein-protein
- K–L · 1058 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 1052 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1051 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1YJX · Crystal structure of human B type phosphoglycerate mutase · the same entry in another collection · chain L against L, 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 P18669
- Elsewhere: RCSB PDB 1YJX · PDBe 1YJX · UniProt P18669
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