Research workbench
Crystal structure of fumarate LYASE:DELTA crystallin from brucella melitensis in native form
Analyse Crystal structure of fumarate LYASE:DELTA crystallin from brucella melitensis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OCF
- Type
- protein
- Length
- 1,748 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate LYASE:DELTA crystallin
- EC
- 4.3.1.1
- UniProt
- Q2YLW1
- Ligands
- CL
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate LYASE:DELTA crystallin (EC 4.3.1.1) | protein | 444 | 63% helix, 9% strand | Q2YLW1 |
| B | Fumarate LYASE:DELTA crystallin (EC 4.3.1.1) | protein | 430 | 63% helix, 9% strand | Q2YLW1 |
| C | Fumarate LYASE:DELTA crystallin (EC 4.3.1.1) | protein | 444 | 64% helix, 8% strand | Q2YLW1 |
| D | Fumarate LYASE:DELTA crystallin (EC 4.3.1.1) | protein | 430 | 63% helix, 9% strand | Q2YLW1 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.77 | 0.98 | 21 | empty |
| 2 | 85 | 0.75 | 0.98 | 21 | empty |
| 3 | 157 | 0.75 | 0.93 | 27 | EDO |
| 4 | 828 | 0.74 | 0.78 | 74 | empty |
| 5 | 182 | 0.73 | 0.90 | 29 | EDO |
Interfaces
6 interfaces between chains.
- B–D · 2611 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 2555 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 2372 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2355 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2111 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 3OCF · Crystal structure of fumarate lyase:delta crystallin from Brucella melitensis in native… · 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 Q2YLW1
- Elsewhere: RCSB PDB 3OCF · PDBe 3OCF · UniProt Q2YLW1
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