MolNFT v1 · #28665 · protein
The crystal structure of mycobacterium tuberculosis dihydrodipicolinate reductase (RV2773C) in complex with NADH (crystal form C)
1YL7: “The crystal structure of mycobacterium tuberculosis dihydrodipicolinate reductase (RV2773C) in complex with…”. X-ray diffraction, 2 ligands (NAI, MG), 20 pockets (best druggability 0.86). MolNFT v1 #28665 on GenesisL1: 3D structure…
- PDB
- 1YL7
- Type
- protein
- Length
- 1,956 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate reductase
- EC
- 1.3.1.26
- UniProt
- P72024
- Ligands
- NAI, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, H | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 245 | 36% helix, 27% strand | P72024 |
| B, E, F, G | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 244 | 36% helix, 27% strand | P72024 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 6 copies · chains A, B, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.86 | 0.92 | 62 | empty |
| 2 | 653 | 0.83 | 0.88 | 84 | empty |
| 3 | 682 | 0.70 | 0.77 | 73 | NAI |
| 4 | 713 | 0.67 | 0.75 | 62 | empty |
| 5 | 382 | 0.61 | 0.77 | 35 | empty |
Interfaces
14 interfaces between chains.
- E–H · 1560 Ų buried · 29 hydrogen bonds · protein-protein
- F–G · 1552 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1540 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1524 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1318 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1YL7 · the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase… · 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 P72024
- Elsewhere: RCSB PDB 1YL7 · PDBe 1YL7 · UniProt P72024
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