MolNFT v1 · #139811 · protein
SAV0551 with glyoxylate
5XR3 · PROTEIN/NUCLEIC acid deglycase hcha: “SAV0551 with glyoxylate”. X-ray diffraction, 1 ligand (GLV), 20 pockets (best druggability 0.79). MolNFT v1 #139811 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XR3
- Type
- protein
- Length
- 2,295 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PROTEIN/NUCLEIC acid deglycase hcha
- EC
- 3.1.2.-, 3.5.1.124
- UniProt
- P64312
- Ligands
- GLV
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124) | protein | 286 | 38% helix, 17% strand | P64312 |
| B | PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124) | protein | 287 | 37% helix, 16% strand | P64312 |
| C | PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124) | protein | 290 | 39% helix, 16% strand | P64312 |
| D, F | PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124) | protein | 284 | 37% helix, 17% strand | P64312 |
| E | PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124) | protein | 285 | 39% helix, 17% strand | P64312 |
| G | PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124) | protein | 292 | 38% helix, 17% strand | P64312 |
| H | PROTEIN/NUCLEIC acid deglycase hcha (EC 3.1.2.-, 3.5.1.124) | protein | 287 | 38% helix, 16% strand | P64312 |
Ligands and binding sites
- GLV · Glyoxylic acid · ligand · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.79 | 0.81 | 112 | empty |
| 2 | 849 | 0.75 | 0.79 | 61 | empty |
| 3 | 609 | 0.74 | 0.81 | 70 | empty |
| 4 | 624 | 0.72 | 0.79 | 64 | empty |
| 5 | 456 | 0.69 | 0.80 | 43 | empty |
Interfaces
16 interfaces between chains.
- G–H · 1230 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1226 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1206 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1205 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 368 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
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 P64312
- Elsewhere: RCSB PDB 5XR3 · PDBe 5XR3 · UniProt P64312
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