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Crystal structure of ldha in complex with compound NCGC00420737-09 at 2.00 a resolution
Analyse Crystal structure of ldha in complex with compound NCGC00420737-09 at 2.00 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q13
- Type
- protein
- Length
- 1,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase a chain
- EC
- 1.1.1.27
- UniProt
- P00338
- Ligands
- NAI, P8V
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 46% helix, 18% strand | P00338 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- P8V · 2-[5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-3-{3-[(5-methylthiophen-2-yl) ethynyl]phenyl}-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic acid · ligand · 4 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.85 | 0.86 | 104 | NAI, P8V, EDO |
| 2 | 827 | 0.70 | 0.76 | 59 | EDO |
| 3 | 692 | 0.70 | 0.77 | 57 | NAI, P8V, EDO |
| 4 | 603 | 0.69 | 0.77 | 57 | NAI, P8V |
| 5 | 213 | 0.48 | 0.75 | 31 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2880 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 683 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 397 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 116 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6Q13 · Crystal structure of ldha in complex with compound NCGC00420737-09 at 2.00 a resolution · 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 P00338
- Elsewhere: RCSB PDB 6Q13 · PDBe 6Q13 · UniProt P00338
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