Research workbench
Structure of the EXBB/EXBD complex from E. COLI at pH 7.0
Analyse Structure of the EXBB/EXBD complex from E. COLI at pH 7.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SV0
- Type
- protein
- Length
- 2,225 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biopolymer transport protein exbb
- UniProt
- P0ABU8
- Ligands
- CA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 9 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, H | Biopolymer transport protein exbb | protein | 225 | 85% helix, 0% strand | P0ABU8 |
| C | Biopolymer transport protein exbb | protein | 222 | 86% helix, 0% strand | P0ABU8 |
| D | Biopolymer transport protein exbb | protein | 215 | 86% helix, 0% strand | P0ABU8 |
| E | Biopolymer transport protein exbb | protein | 216 | 83% helix, 0% strand | P0ABU8 |
| F | Biopolymer transport protein exbb | protein | 223 | 83% helix, 0% strand | P0ABU8 |
| G | Biopolymer transport protein exbb | protein | 229 | 82% helix, 0% strand | P0ABU8 |
| I | Biopolymer transport protein exbb | protein | 223 | 84% helix, 0% strand | P0ABU8 |
| J | Biopolymer transport protein exbb | protein | 214 | 84% helix, 0% strand | P0ABU8 |
| A | Biopolymer transport protein exbb | protein | 233 | 80% helix, 0% strand | P0ABU8 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains I, J, B, C, F, A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains C, D, E, F, G, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 683 | 0.74 | 0.80 | 63 | empty |
| 2 | 943 | 0.68 | 0.73 | 74 | empty |
| 3 | 939 | 0.68 | 0.73 | 82 | empty |
| 4 | 477 | 0.64 | 0.77 | 40 | empty |
| 5 | 359 | 0.62 | 0.78 | 42 | empty |
Interfaces
14 interfaces between chains.
- G–H · 1602 Ų buried · 15 hydrogen bonds · protein-protein
- F–A · 1594 Ų buried · 16 hydrogen bonds · protein-protein
- B–A · 1526 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 1498 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1495 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (methylation).
Compared structures
- 5SV0 · Structure of the ExbB/ExbD complex from E. coli at pH 7.0 · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABU8 · AlphaFold monomer V2.0 prediction for biopolymer transport protein exbb (P0ABU8) · 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 P0ABU8
- Elsewhere: RCSB PDB 5SV0 · PDBe 5SV0 · UniProt P0ABU8
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