MolNFT v1 · #141274 · protein
The ternary structure of D-lactate dehydrogenase from pseudomonas aeruginosa with NADH and oxamate
5Z20 · D-lactate dehydrogenase (fermentative): “The ternary structure of D-lactate dehydrogenase from pseudomonas aeruginosa with NADH and oxamate”. X-ray diffraction, 2 ligands (NAI, OXM), 17 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5Z20
- Type
- protein
- Length
- 1,989 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lactate dehydrogenase (fermentative)
- EC
- 1.1.1.28
- UniProt
- Q9I530
- Ligands
- NAI, OXM
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | D-lactate dehydrogenase (fermentative) (EC 1.1.1.28) | protein | 330 | 37% helix, 17% strand | Q9I530 |
| B | D-lactate dehydrogenase (fermentative) (EC 1.1.1.28) | protein | 334 | 38% helix, 17% strand | Q9I530 |
| D | D-lactate dehydrogenase (fermentative) (EC 1.1.1.28) | protein | 329 | 39% helix, 17% strand | Q9I530 |
| F | D-lactate dehydrogenase (fermentative) (EC 1.1.1.28) | protein | 336 | 38% helix, 17% strand | Q9I530 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- OXM · Oxamic acid · ligand · 6 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 4 copies · chains A, C, D, F
- FMT · Formic acid · additive · 2 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.84 | 0.87 | 123 | FMT |
| 2 | 1021 | 0.74 | 0.77 | 100 | NAI, OXM |
| 3 | 322 | 0.70 | 0.83 | 43 | NAI, OXM |
| 4 | 343 | 0.69 | 0.82 | 44 | NAI, OXM |
| 5 | 294 | 0.68 | 0.83 | 42 | NAI, OXM |
Interfaces
9 interfaces between chains.
- A–B · 2755 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2727 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 2713 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 900 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 893 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5Z20 · The ternary structure of D-lactate dehydrogenase from Pseudomonas aeruginosa with NADH… · 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 Q9I530
- Elsewhere: RCSB PDB 5Z20 · PDBe 5Z20 · UniProt Q9I530
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