MolNFT v1 · #86477 · protein
Plasmodium falciparum L-lactate dehydrogenase complexed with bicine
4B7U: “Plasmodium falciparum L-lactate dehydrogenase complexed with bicine”. X-ray diffraction, 2 ligands (BCN, CA), 16 pockets (best druggability 0.81). MolNFT v1 #86477 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4B7U
- Type
- protein
- Length
- 1,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q71T02
- Ligands
- BCN, CA
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 316 | 49% helix, 20% strand | Q71T02 |
| B, C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 305 | 50% helix, 21% strand | Q71T02 |
| D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 306 | 50% helix, 21% strand | Q71T02 |
Ligands and binding sites
- BCN · Bicine · ligand · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.81 | 0.96 | 43 | empty |
| 2 | 163 | 0.81 | 0.97 | 43 | empty |
| 3 | 614 | 0.81 | 0.86 | 58 | empty |
| 4 | 216 | 0.72 | 0.88 | 26 | empty |
| 5 | 295 | 0.71 | 0.85 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2223 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2192 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1288 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1259 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 614 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4B7U · Plasmodium falciparum L-lactate dehydrogenase complexed with bicine · 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 Q71T02
- Elsewhere: RCSB PDB 4B7U · PDBe 4B7U · UniProt Q71T02
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