Research workbench
Structure of the EXBB/EXBD pentameric complex (EXBB5EXBD1TM)
Analyse Structure of the EXBB/EXBD pentameric complex (EXBB5EXBD1TM) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZFV
- Type
- protein
- Length
- 1,133 residues
- Chains
- 6
- 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 0.91
Structure
electron microscopy · 6 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biopolymer transport protein exbb | protein | 224 | 79% helix, 0% strand | P0ABU7 |
| B | Biopolymer transport protein exbb | protein | 225 | 80% helix, 0% strand | P0ABU7 |
| C | Biopolymer transport protein exbb | protein | 224 | 83% helix, 0% strand | P0ABU7 |
| D | Biopolymer transport protein exbb | protein | 215 | 83% helix, 0% strand | P0ABU7 |
| E | Biopolymer transport protein exbb | protein | 223 | 79% helix, 0% strand | P0ABU7 |
| F | 22-mer peptide from biopolymer transport protein exbd | protein | 22 | 59% helix, 0% strand | P0ABV2 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.91 | 0.93 | 128 | empty |
| 2 | 573 | 0.70 | 0.79 | 70 | empty |
| 3 | 580 | 0.68 | 0.78 | 71 | empty |
| 4 | 331 | 0.67 | 0.82 | 47 | empty |
| 5 | 126 | 0.65 | 0.87 | 19 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1448 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1417 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1364 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1289 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1173 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5ZFV · Structure of the ExbB/ExbD pentameric complex (ExbB5ExbD1TM) · the same entry in another collection · chain F against F, TM-score 1.00
- P0ABU7 · AlphaFold monomer V2.0 prediction for biopolymer transport protein exbb (P0ABU7) · a predicted model of the same protein · chain C against A, TM-score 0.93
- P0ABV2 · AlphaFold monomer V2.0 prediction for biopolymer transport protein exbd (P0ABV2) · a predicted model of the same protein · chain F against A, TM-score 0.42
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 5ZFV · PDBe 5ZFV · UniProt P0ABU7 · UniProt P0ABV2
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