Research workbench
Crystal structure of sbnh in complex with citrate, a plp-dependent decarboxylase in staphyloferrin B biothesynthesis
Analyse Crystal structure of sbnh in complex with citrate, a plp-dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KNH
- Type
- protein
- Length
- 1,149 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable diaminopimelate decarboxylase protein
- UniProt
- A0A0H3JPF2
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable diaminopimelate decarboxylase protein | protein | 383 | 36% helix, 28% strand | A0A0H3JPF2 |
| B | Probable diaminopimelate decarboxylase protein | protein | 382 | 35% helix, 28% strand | A0A0H3JPF2 |
| C | Probable diaminopimelate decarboxylase protein | protein | 384 | 35% helix, 28% strand | A0A0H3JPF2 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- CIT · Citric acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.82 | 0.85 | 110 | CIT, PO4 |
| 2 | 503 | 0.66 | 0.77 | 58 | empty |
| 3 | 449 | 0.62 | 0.76 | 37 | empty |
| 4 | 146 | 0.61 | 0.85 | 23 | empty |
| 5 | 231 | 0.59 | 0.80 | 41 | PO4 |
Interfaces
3 interfaces between chains.
- A–B · 3098 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 631 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6KNH · Crystal structure of SbnH in complex with citrate, a PLP-dependent decarboxylase in… · 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 A0A0H3JPF2
- Elsewhere: RCSB PDB 6KNH · PDBe 6KNH · UniProt A0A0H3JPF2
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