MolNFT v1 · #134877 · protein
Crystal structure of fumarylacetoacetate hydrolase from burkholderia xenovorans LB400
5TI1: “Crystal structure of fumarylacetoacetate hydrolase from burkholderia xenovorans LB400”. X-ray diffraction, 4 ligands (MG, NA, NO3), 20 pockets (best druggability 0.80). MolNFT v1 #134877 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5TI1
- Type
- protein
- Length
- 3,430 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarylacetoacetate hydrolase
- EC
- 3.7.1.2
- UniProt
- Q144Z1
- Ligands
- MG, NA, NO3, PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarylacetoacetate hydrolase (EC 3.7.1.2) | protein | 426 | 25% helix, 28% strand | Q144Z1 |
| B, C, D, F | Fumarylacetoacetate hydrolase (EC 3.7.1.2) | protein | 429 | 26% helix, 28% strand | Q144Z1 |
| E, G | Fumarylacetoacetate hydrolase (EC 3.7.1.2) | protein | 429 | 26% helix, 28% strand | Q144Z1 |
| H | Fumarylacetoacetate hydrolase (EC 3.7.1.2) | protein | 430 | 27% helix, 28% strand | Q144Z1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- NO3 · Nitrate ion · ion · 7 copies · chains C, D, E, F, G, H
- PO4 · Phosphate ion · ion · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.80 | 0.81 | 113 | empty |
| 2 | 1171 | 0.77 | 0.79 | 122 | empty |
| 3 | 876 | 0.74 | 0.78 | 78 | empty |
| 4 | 228 | 0.73 | 0.88 | 36 | NO3 |
| 5 | 225 | 0.73 | 0.88 | 38 | NO3 |
Interfaces
12 interfaces between chains.
- A–B · 2773 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2769 Ų buried · 44 hydrogen bonds · protein-protein
- G–H · 2760 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2758 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 1031 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5TI1 · Crystal Structure of Fumarylacetoacetate hydrolase from Burkholderia xenovorans LB400 · 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 Q144Z1
- Elsewhere: RCSB PDB 5TI1 · PDBe 5TI1 · UniProt Q144Z1
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