Research workbench
Crystal structure of a short chain dehydrogenase homolog (target efi- 505321) from burkholderia multivorans, unliganded structure
Analyse Crystal structure of a short chain dehydrogenase homolog (target efi- 505321)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GKB
- Type
- protein
- Length
- 1,013 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier protein] reductase
- EC
- 1.1.1.100
- UniProt
- A9ANE0
- Ligands
- CA, CL
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | protein | 247 | 47% helix, 15% strand | A9ANE0 |
| B, C | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | protein | 258 | 48% helix, 14% strand | A9ANE0 |
| D | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | protein | 250 | 48% helix, 15% strand | A9ANE0 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, D, C, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.86 | 0.91 | 40 | EDO |
| 2 | 379 | 0.78 | 0.87 | 45 | CL |
| 3 | 605 | 0.73 | 0.80 | 53 | empty |
| 4 | 626 | 0.72 | 0.80 | 59 | CL |
| 5 | 420 | 0.71 | 0.82 | 53 | CL |
Interfaces
6 interfaces between chains.
- A–B · 1827 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1809 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1600 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1579 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 687 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4GKB · Crystal structure of a short chain dehydrogenase homolog (target efi-505321) from… · 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 A9ANE0
- Elsewhere: RCSB PDB 4GKB · PDBe 4GKB · UniProt A9ANE0
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