Research workbench
Crystal structure of lactate dehydrogenase from thermus thermophilus HB8 (holo form)
Analyse Crystal structure of lactate dehydrogenase from thermus thermophilus HB8 (holo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V7P
- Type
- protein
- Length
- 1,219 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
- Ligands
- OXM, NAD
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 310 | 49% helix, 22% strand | Q5SJA1 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 299 | 48% helix, 22% strand | Q5SJA1 |
| D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 300 | 48% helix, 24% strand | Q5SJA1 |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.83 | 0.92 | 61 | empty |
| 2 | 313 | 0.81 | 0.91 | 47 | empty |
| 3 | 153 | 0.70 | 0.89 | 25 | empty |
| 4 | 165 | 0.69 | 0.88 | 31 | OXM, NAD |
| 5 | 137 | 0.68 | 0.89 | 28 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2321 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2258 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1084 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1077 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 262 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2V7P · Crystal structure of lactate dehydrogenase from Thermus Thermophilus HB8 (Holo 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 D 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 2V7P · PDBe 2V7P · UniProt Q5SJA1
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