Research workbench
Derivative structure of the udp-N-acetyl-mannosamine dehydrogenase CAP5O from S. aureus
Analyse Derivative 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
- 3OJO
- Type
- protein
- Length
- 827 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAP5O
- UniProt
- P95708
- Ligands
- PDC, NAD, EU
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CAP5O | protein | 409 | 39% helix, 16% strand | P95708 |
| B | CAP5O | protein | 418 | 41% helix, 15% strand | P95708 |
Ligands and binding sites
- PDC · Pyridine-2,6-dicarboxylic acid · ligand · 6 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- EU · Europium ion · metal · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.78 | 0.81 | 66 | NAD, PDC, EU |
| 2 | 1050 | 0.75 | 0.78 | 84 | EU, PDC, NAD |
| 3 | 105 | 0.53 | 0.83 | 19 | empty |
| 4 | 114 | 0.49 | 0.81 | 19 | empty |
| 5 | 114 | 0.44 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2151 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3OJO · Derivative structure of the UDP-N-acetyl-mannosamine dehydrogenase Cap5O from S. aureus · 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 P95708
- Elsewhere: RCSB PDB 3OJO · PDBe 3OJO · UniProt P95708
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