MolNFT v1 · #51406 · protein
Crystal structure of lactate dehydrogenase from thermus thermophilus HB8 (apo form)
2V6M · L-lactate dehydrogenase: “Crystal structure of lactate dehydrogenase from thermus thermophilus HB8 (apo form)”. X-ray diffraction, 8 pockets (best druggability 0.81). MolNFT v1 #51406 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2V6M
- Type
- protein
- Length
- 1,226 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
- Q5SJA1
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 310 | 48% helix, 24% strand | Q5SJA1 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 303 | 48% helix, 22% strand | Q5SJA1 |
| D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 303 | 49% helix, 22% strand | Q5SJA1 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.81 | 0.83 | 83 | MES |
| 2 | 906 | 0.81 | 0.83 | 80 | MES |
| 3 | 502 | 0.65 | 0.77 | 63 | empty |
| 4 | 431 | 0.65 | 0.78 | 53 | empty |
| 5 | 265 | 0.60 | 0.79 | 51 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1823 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1801 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 904 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 853 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2V6M · Crystal structure of lactate dehydrogenase from Thermus Thermophilus HB8 (Apo form) · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SJA1 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (Q5SJA1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5SJA1
- Elsewhere: RCSB PDB 2V6M · PDBe 2V6M · UniProt Q5SJA1
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