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Crystal structure of dihydrodipicolinate synthase (dapa, RV2753C) from mycobacterium tuberculosis
Analyse Crystal structure of dihydrodipicolinate synthase (dapa, RV2753C) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XXX
- Type
- protein
- Length
- 2,364 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- P63945
- Ligands
- MG, CL
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, H | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 296 | 52% helix, 13% strand | P63945 |
| B, D, E, G | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 295 | 54% helix, 13% strand | P63945 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.73 | 0.81 | 92 | DTT |
| 2 | 250 | 0.67 | 0.84 | 51 | empty |
| 3 | 235 | 0.64 | 0.83 | 43 | empty |
| 4 | 646 | 0.62 | 0.73 | 64 | empty |
| 5 | 242 | 0.60 | 0.80 | 41 | DTT |
Interfaces
9 interfaces between chains.
- E–F · 1501 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1500 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1499 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1494 Ų buried · 25 hydrogen bonds · protein-protein
- E–H · 893 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (additive adduct).
Compared structures
- 1XXX · Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium… · 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 1XXX · PDBe 1XXX · UniProt P63945
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