MolNFT v1 · #128778 · protein
Crystal structure of the complex between NB474 and trypanosoma congolense fructose-1,6-bisphosphate aldolase
5O0W · Fructose-bisphosphate aldolase: “Crystal structure of the complex between NB474 and trypanosoma congolense fructose-1,6-bisphosphate aldolase”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #128778 on GenesisL1…
- PDB
- 5O0W
- Type
- protein
- Length
- 1,985 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-bisphosphate aldolase; NB474
- EC
- 4.1.2.13
- UniProt
- G0UWE7
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 360 | 47% helix, 16% strand | G0UWE7 |
| B | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 358 | 48% helix, 16% strand | G0UWE7 |
| D | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 359 | 47% helix, 16% strand | G0UWE7 |
| E, F | NB474 | protein | 137 | 7% helix, 45% strand | — |
| G | NB474 | protein | 138 | 7% helix, 45% strand | — |
| H | NB474 | protein | 136 | 4% helix, 46% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.88 | 0.89 | 142 | GOL |
| 2 | 264 | 0.75 | 0.88 | 42 | empty |
| 3 | 255 | 0.75 | 0.88 | 41 | empty |
| 4 | 280 | 0.62 | 0.80 | 36 | GOL |
| 5 | 308 | 0.62 | 0.80 | 44 | GOL |
Interfaces
10 interfaces between chains.
- A–C · 1431 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1421 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1387 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1385 Ų buried · 14 hydrogen bonds · protein-protein
- C–G · 764 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5O0W · Crystal structure of the complex between Nb474 and Trypanosoma congolense… · 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 G0UWE7
- Elsewhere: RCSB PDB 5O0W · PDBe 5O0W · UniProt G0UWE7
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