MolNFT v1 · #34078 · protein
Crystal structure of the hpcc from thermus thermophilus HB8
2D4E · 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase: “Crystal structure of the hpcc from thermus thermophilus HB8”. X-ray diffraction, 2 ligands (NAD, NA), 16 pockets (best druggability 0.86). MolNFT v1 #34078 on GenesisL1…
- PDB
- 2D4E
- Type
- protein
- Length
- 2,056 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
- EC
- 1.2.1.60
- Ligands
- NAD, NA
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60) | protein | 513 | 42% helix, 21% strand | — |
| C, D | 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60) | protein | 515 | 42% helix, 21% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains C, D
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.86 | 0.87 | 119 | empty |
| 2 | 528 | 0.84 | 0.90 | 89 | empty |
| 3 | 998 | 0.81 | 0.82 | 94 | empty |
| 4 | 557 | 0.80 | 0.86 | 66 | NA, NAD |
| 5 | 518 | 0.79 | 0.86 | 59 | NA, NAD |
Interfaces
6 interfaces between chains.
- A–B · 3844 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 3629 Ų buried · 53 hydrogen bonds · protein-protein
- B–D · 1363 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1330 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 907 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2D4E · Crystal Structure of the HpcC from Thermus Thermophilus HB8 · 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
- Elsewhere: RCSB PDB 2D4E · PDBe 2D4E
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