Research workbench
Cryo-EM structure of lactate dehydrogenase (ldh) in inhibitor-bound state
Analyse Cryo-EM structure of lactate dehydrogenase (ldh) in inhibitor-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K0Z
- Type
- protein
- Length
- 1,268 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase B chain
- EC
- 1.1.1.27
- UniProt
- P00337
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-lactate dehydrogenase B chain (EC 1.1.1.27) | protein | 317 | 40% helix, 21% strand | P00337 |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.83 | 0.92 | 48 | empty |
| 2 | 350 | 0.81 | 0.91 | 47 | empty |
| 3 | 110 | 0.64 | 0.89 | 34 | empty |
| 4 | 125 | 0.56 | 0.83 | 25 | empty |
| 5 | 113 | 0.55 | 0.84 | 26 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2819 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2818 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1454 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1445 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 967 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5K0Z · Cryo-EM structure of lactate dehydrogenase (LDH) in inhibitor-bound state · the same entry in another collection · chain A against A, TM-score 1.00
- P00337 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase B chain (P00337) · a predicted model of the same protein · chain A 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 P00337
- Elsewhere: RCSB PDB 5K0Z · PDBe 5K0Z · UniProt P00337
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