Research workbench
Crystal structure of GDP-mannose 4,6-dehydratase from brucella abortus (strain 2308) in complex with guanosine-diphosphate-rhamnose
Analyse Crystal structure of GDP-mannose 4,6-dehydratase from brucella abortus (strain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KF3
- Type
- protein
- Length
- 1,448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-mannose 4,6-dehydratase
- EC
- 4.2.1.47
- UniProt
- Q2YMP3
- Ligands
- GDR, NAP
- Pockets
- 12 · best druggability 0.91
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | GDP-mannose 4,6-dehydratase (EC 4.2.1.47) | protein | 362 | 42% helix, 17% strand | Q2YMP3 |
Ligands and binding sites
- GDR · Guanosine-5'-diphosphate-rhamnose · ligand · 4 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.91 | 0.94 | 132 | GDR, NAP |
| 2 | 1162 | 0.91 | 0.94 | 148 | GDR, NAP |
| 3 | 106 | 0.78 | 0.98 | 30 | empty |
| 4 | 190 | 0.70 | 0.88 | 37 | empty |
| 5 | 56 | 0.59 | 0.91 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2286 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2282 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1353 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1348 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 474 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7KF3 · Crystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in… · 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 Q2YMP3
- Elsewhere: RCSB PDB 7KF3 · PDBe 7KF3 · UniProt Q2YMP3
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