MolNFT v1 · #137769 · protein
Crystal structure of the wbkc formyl transferase from brucella melitensis
5VYR · GDP-mannose 4,6-dehydratase / GDP-4-amino-4,6-dideoxy-D…: “Crystal structure of the wbkc formyl transferase from brucella melitensis”. X-ray diffraction, 3 ligands (GMP, B62, CL), 5 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 5VYR
- Type
- protein
- Length
- 489 residues
- Chains
- 2
- 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
- GMP, B62, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 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 | 244 | 36% helix, 20% 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 | 245 | 35% helix, 21% strand | F8WJP6 |
Ligands and binding sites
- GMP · Guanosine · ligand · 3 copies · chains A, B
- B62 · (6R)-2-amino-6-methyl-5,6,7,8-tetrahydropteridin-4(3H)-one · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.77 | 0.83 | 59 | B62, GMP |
| 2 | 558 | 0.76 | 0.83 | 53 | B62, GMP |
| 3 | 191 | 0.51 | 0.77 | 29 | empty |
| 4 | 159 | 0.47 | 0.76 | 31 | empty |
| 5 | 55 | 0.29 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1564 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5VYR · Crystal structure of the WbkC formyl transferase 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 5VYR · PDBe 5VYR · UniProt F8WJP6
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