Research workbench
Crystal structure of the N-acetyl-D-mannosamine dehydrogenase with NAD
Analyse Crystal structure of the N-acetyl-D-mannosamine dehydrogenase with NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CR8
- Type
- protein
- Length
- 2,099 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylmannosamine 1-dehydrogenase
- EC
- 1.1.1.233
- UniProt
- P22441
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233) | protein | 263 | 46% helix, 15% strand | P22441 |
| C, E, F, G | N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233) | protein | 262 | 46% helix, 15% strand | P22441 |
| D | N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233) | protein | 264 | 46% helix, 16% strand | P22441 |
| H | N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233) | protein | 261 | 46% helix, 15% strand | P22441 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.86 | 0.87 | 75 | empty |
| 2 | 619 | 0.75 | 0.82 | 60 | NAD |
| 3 | 513 | 0.73 | 0.81 | 56 | NAD |
| 4 | 491 | 0.68 | 0.78 | 52 | NAD |
| 5 | 529 | 0.68 | 0.78 | 51 | NAD |
Interfaces
16 interfaces between chains.
- D–F · 1838 Ų buried · 30 hydrogen bonds · protein-protein
- C–E · 1833 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1602 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1598 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1597 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4CR8 · Crystal structure of the N-acetyl-D-mannosamine dehydrogenase with NAD · the same entry in another collection · chain H against H, TM-score 1.00
- P22441 · AlphaFold monomer V2.0 prediction for N-acylmannosamine 1-dehydrogenase (P22441) · a predicted model of the same protein · chain H 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 P22441
- Elsewhere: RCSB PDB 4CR8 · PDBe 4CR8 · UniProt P22441
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