Research workbench
Structure and assembly of a B-propeller with nine blades and a new conserved repetitive sequence motif
Analyse Structure and assembly of a B-propeller with nine blades and a new conserved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YMS
- Type
- protein
- Length
- 347 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bamb
- UniProt
- P77774
- Ligands
- NA
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bamb | protein | 124 | 0% helix, 53% strand | P77774 |
| B | Outer membrane protein assembly factor bamb | protein | 74 | 0% helix, 55% strand | P77774 |
| C | Outer membrane protein assembly factor bamb | protein | 75 | 0% helix, 57% strand | P77774 |
| D | Outer membrane protein assembly factor bamb | protein | 74 | 0% helix, 54% strand | P77774 |
Ligands and binding sites
- NA · Sodium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.43 | 0.80 | 23 | empty |
| 2 | 62 | 0.29 | 0.74 | 12 | empty |
Interfaces
4 interfaces between chains.
- A–C · 841 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 690 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 687 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 570 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2YMS · Structure and assembly of a b-propeller with nine blades and a new conserved repetitive… · the same entry in another collection · chain D against D, TM-score 1.00
- P77774 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamb (P77774) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P77774
- Elsewhere: RCSB PDB 2YMS · PDBe 2YMS · UniProt P77774
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