Research workbench
Native structure of the udp-N-acetyl-mannosamine dehydrogenase CAP5O from staphylococcus aureus
Analyse Native structure of the udp-N-acetyl-mannosamine dehydrogenase CAP5O from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OJL
- Type
- protein
- Length
- 830 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAP5O
- UniProt
- P95708
- Ligands
- NAD
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CAP5O | protein | 418 | 40% helix, 14% strand | P95708 |
| B | CAP5O | protein | 412 | 39% helix, 16% strand | P95708 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.76 | 0.79 | 94 | NAD |
| 2 | 1125 | 0.76 | 0.78 | 91 | NAD |
| 3 | 97 | 0.34 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2301 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3OJL · Native structure of the UDP-N-acetyl-mannosamine dehydrogenase Cap5O from Staphylococcus… · the same entry in another collection · chain B against B, 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 P95708
- Elsewhere: RCSB PDB 3OJL · PDBe 3OJL · UniProt P95708
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