Research workbench
Structure of the N-terminal domain of bamc from E. COLI
Analyse Structure of the N-terminal domain of bamc from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YH6
- Type
- protein
- Length
- 434 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein 34
- UniProt
- P0A903
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein 34 | protein | 108 | 32% helix, 43% strand | P0A903 |
| B | Lipoprotein 34 | protein | 107 | 32% helix, 38% strand | P0A903 |
| C | Lipoprotein 34 | protein | 109 | 34% helix, 41% strand | P0A903 |
| D | Lipoprotein 34 | protein | 110 | 34% helix, 41% strand | P0A903 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.51 | 0.73 | 37 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1016 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1011 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 105 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 103 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YH6 · Structure of the N-terminal domain of BamC from E. coli · the same entry in another collection · chain D against D, TM-score 1.00
- P0A903 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamc (P0A903) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P0A903
- Elsewhere: RCSB PDB 2YH6 · PDBe 2YH6 · UniProt P0A903
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