Research workbench
Crystal structure of the wbkc N-formyltransferase (F142A variant) from brucella melitensis
Analyse Crystal structure of the wbkc N-formyltransferase (F142A variant) from brucella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VYT
- Type
- protein
- Length
- 1,006 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-mannose 4,6-dehydratase / GDP-4-amino-4,6-dideoxy-D- mannose formyltransferase
- EC
- 2.1.2.-, 4.2.1.47
- UniProt
- F8WJP6
- Ligands
- FON, GDP, CL
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-mannose 4,6-dehydratase / GDP-4-amino-4,6-dideoxy-D- mannose formyltransferase (EC 2.1.2.-, 4.2.1.47) | protein | 248 | 37% helix, 19% strand | F8WJP6 |
| B | GDP-mannose 4,6-dehydratase / GDP-4-amino-4,6-dideoxy-D- mannose formyltransferase (EC 2.1.2.-, 4.2.1.47) | protein | 252 | 37% helix, 19% strand | F8WJP6 |
| C | GDP-mannose 4,6-dehydratase / GDP-4-amino-4,6-dideoxy-D- mannose formyltransferase (EC 2.1.2.-, 4.2.1.47) | protein | 256 | 36% helix, 21% strand | F8WJP6 |
| D | GDP-mannose 4,6-dehydratase / GDP-4-amino-4,6-dideoxy-D- mannose formyltransferase (EC 2.1.2.-, 4.2.1.47) | protein | 250 | 36% helix, 22% strand | F8WJP6 |
Ligands and binding sites
- FON · N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid · ligand · 4 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.75 | 0.81 | 63 | FON, GDP |
| 2 | 555 | 0.75 | 0.82 | 51 | FON, GDP |
| 3 | 76 | 0.73 | 0.96 | 16 | empty |
| 4 | 546 | 0.72 | 0.81 | 55 | FON, GDP |
| 5 | 519 | 0.72 | 0.81 | 54 | FON, GDP |
Interfaces
3 interfaces between chains.
- A–B · 1629 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1562 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 483 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5VYT · Crystal structure of the WbkC N-formyltransferase (F142A variant) from Brucella melitensis · 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 F8WJP6
- Elsewhere: RCSB PDB 5VYT · PDBe 5VYT · UniProt F8WJP6
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