Research workbench
Structure of the EXBB/EXBD hexameric complex (EXBB6EXBD3TM)
Analyse Structure of the EXBB/EXBD hexameric complex (EXBB6EXBD3TM) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZFU
- Type
- protein
- Length
- 1,382 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biopolymer transport protein exbb; 22-mer peptide from biopolymer transport protein exbd
- UniProt
- P0ABU7, P0ABV2
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biopolymer transport protein exbb | protein | 225 | 85% helix, 0% strand | P0ABU7 |
| B | Biopolymer transport protein exbb | protein | 215 | 84% helix, 0% strand | P0ABU7 |
| C | Biopolymer transport protein exbb | protein | 223 | 82% helix, 0% strand | P0ABU7 |
| D | Biopolymer transport protein exbb | protein | 215 | 83% helix, 0% strand | P0ABU7 |
| E | Biopolymer transport protein exbb | protein | 222 | 86% helix, 0% strand | P0ABU7 |
| F | Biopolymer transport protein exbb | protein | 216 | 82% helix, 0% strand | P0ABU7 |
| G, H, I | 22-mer peptide from biopolymer transport protein exbd | protein | 22 | 68% helix, 0% strand | P0ABV2 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.85 | 0.85 | 122 | empty |
| 2 | 716 | 0.80 | 0.84 | 87 | empty |
| 3 | 162 | 0.78 | 0.94 | 32 | empty |
| 4 | 619 | 0.67 | 0.77 | 60 | empty |
| 5 | 154 | 0.67 | 0.88 | 35 | empty |
Interfaces
18 interfaces between chains.
- A–B · 1483 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1460 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 1457 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1368 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1354 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5ZFU · Structure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM) · the same entry in another collection · chain I against I, TM-score 1.00
- P0ABU7 · AlphaFold monomer V2.0 prediction for biopolymer transport protein exbb (P0ABU7) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 P0ABU7
- Every structure of UniProt P0ABV2
- Elsewhere: RCSB PDB 5ZFU · PDBe 5ZFU · UniProt P0ABU7 · UniProt P0ABV2
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