Research workbench
The crystal structure of a dimeric mutant of dihydrodipicolinate synthase (dapa, RV2753C) from mycobacterium tuberculosis - dhdps- A204R
Analyse The crystal structure of a dimeric mutant of dihydrodipicolinate synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L21
- Type
- protein
- Length
- 1,772 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- P63945
- Ligands
- PYR, SO4, CL
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 297 | 53% helix, 13% strand | P63945 |
| B, C, D, E, F | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 295 | 53% helix, 13% strand | P63945 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · chains B
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 3 copies · chains D, E
- GOL · Glycerol · additive · 26 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 11 copies · chains A, C, D, B, E, F
- BME · Beta-mercaptoethanol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.83 | 0.84 | 127 | ACT, BME, SO4, GOL |
| 2 | 1076 | 0.82 | 0.83 | 101 | empty |
| 3 | 280 | 0.68 | 0.83 | 53 | SO4, GOL |
| 4 | 275 | 0.67 | 0.83 | 57 | GOL, SO4 |
| 5 | 267 | 0.66 | 0.83 | 43 | ACT, GOL |
Interfaces
9 interfaces between chains.
- E–F · 1515 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1507 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1504 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 455 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 386 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (artifact, nonstandard).
Compared structures
- 3L21 · The crystal structure of a dimeric mutant of dihydrodipicolinate synthase (DAPA, RV2753C)… · the same entry in another collection · chain A against A, 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 P63945
- Elsewhere: RCSB PDB 3L21 · PDBe 3L21 · UniProt P63945
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.