Research workbench
Crystal structure of a citrate lyase (BXE_B2899) from burkholderia xenovorans LB400 at 2.24 a resolution
Analyse Crystal structure of a citrate lyase (BXE_B2899) from burkholderia xenovorans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R4I
- Type
- protein
- Length
- 1,914 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate lyase
- EC
- 4.1.3.6
- UniProt
- Q13S43
- Ligands
- CA, CL
- Pockets
- 19 · best druggability 0.54
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Citrate lyase (EC 4.1.3.6) | protein | 321 | 49% helix, 13% strand | Q13S43 |
| B | Citrate lyase (EC 4.1.3.6) | protein | 319 | 49% helix, 13% strand | Q13S43 |
| C | Citrate lyase (EC 4.1.3.6) | protein | 320 | 49% helix, 13% strand | Q13S43 |
| D, F | Citrate lyase (EC 4.1.3.6) | protein | 317 | 50% helix, 14% strand | Q13S43 |
| E | Citrate lyase (EC 4.1.3.6) | protein | 320 | 49% helix, 13% strand | Q13S43 |
Ligands and binding sites
- CA · Calcium ion · metal · 13 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 5 copies · chains B, C, D, E, F
- ACT · Acetate ion · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.54 | 0.82 | 30 | CA, CL, ACT |
| 2 | 141 | 0.54 | 0.81 | 32 | CA, CL |
| 3 | 323 | 0.54 | 0.74 | 33 | empty |
| 4 | 305 | 0.53 | 0.75 | 27 | empty |
| 5 | 97 | 0.53 | 0.84 | 22 | CA |
Interfaces
7 interfaces between chains.
- A–B · 402 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 234 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 176 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3R4I · Crystal structure of a Citrate lyase (Bxe_B2899) from BURKHOLDERIA XENOVORANS LB400 at… · 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 Q13S43
- Elsewhere: RCSB PDB 3R4I · PDBe 3R4I · UniProt Q13S43
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.