Research workbench
Cryo-EM structure of exbbd from serratia marcescens
Analyse Cryo-EM structure of exbbd from serratia marcescens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AJQ
- Type
- protein
- Length
- 1,222 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biopolymer transport protein exbb; Biopolymer transport protein exbd
- UniProt
- A0A542C9I8, V5YUQ0
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biopolymer transport protein exbb | protein | 230 | 84% helix, 0% strand | A0A542C9I8 |
| B, C, D, E | Biopolymer transport protein exbb | protein | 236 | 83% helix, 0% strand | A0A542C9I8 |
| F | Biopolymer transport protein exbd | protein | 23 | 65% helix, 0% strand | V5YUQ0 |
| G | Biopolymer transport protein exbd | protein | 25 | 64% helix, 0% strand | V5YUQ0 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.83 | 0.88 | 87 | empty |
| 2 | 243 | 0.80 | 0.92 | 39 | empty |
| 3 | 160 | 0.79 | 0.95 | 27 | empty |
| 4 | 475 | 0.69 | 0.80 | 56 | empty |
| 5 | 134 | 0.69 | 0.90 | 34 | empty |
Interfaces
15 interfaces between chains.
- D–E · 1674 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1616 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1508 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1467 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 1412 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7AJQ · cryo-EM structure of ExbBD from Serratia Marcescens · 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 A0A542C9I8
- Every structure of UniProt V5YUQ0
- Elsewhere: RCSB PDB 7AJQ · PDBe 7AJQ · UniProt A0A542C9I8 · UniProt V5YUQ0
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