Research workbench
Structure of the periplasmic domain of the heparin and heparan sulphate sensing hybrid two component system BT4663 in apo and ligand bound forms
Analyse Structure of the periplasmic domain of the heparin and heparan sulphate sensing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A2L
- Type
- protein
- Length
- 4,478 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Two-component system sensor histidine KINASE/RESPONSE
- UniProt
- Q89YR8
- Ligands
- OAA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Two-component system sensor histidine KINASE/RESPONSE | protein | 747 | 4% helix, 48% strand | Q89YR8 |
| B | Two-component system sensor histidine KINASE/RESPONSE | protein | 744 | 4% helix, 48% strand | Q89YR8 |
| C | Two-component system sensor histidine KINASE/RESPONSE | protein | 749 | 4% helix, 48% strand | Q89YR8 |
| D | Two-component system sensor histidine KINASE/RESPONSE | protein | 745 | 4% helix, 48% strand | Q89YR8 |
| E | Two-component system sensor histidine KINASE/RESPONSE | protein | 744 | 3% helix, 49% strand | Q89YR8 |
| F | Two-component system sensor histidine KINASE/RESPONSE | protein | 749 | 4% helix, 47% strand | Q89YR8 |
Ligands and binding sites
- OAA · Oxaloacetate ion · ligand · 3 copies · chains C, E
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, E, F
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, C, D, E, F
- PG4 · Tetraethylene glycol · additive · chains B
- 2PE · Nonaethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.78 | 0.80 | 75 | empty |
| 2 | 1120 | 0.78 | 0.80 | 88 | MES |
| 3 | 794 | 0.77 | 0.81 | 73 | MES |
| 4 | 440 | 0.77 | 0.86 | 54 | empty |
| 5 | 980 | 0.76 | 0.78 | 81 | EDO, MES |
Interfaces
9 interfaces between chains.
- C–D · 2232 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2153 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2066 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 715 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 686 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4A2L · Structure of the periplasmic domain of the heparin and heparan sulphate sensing hybrid… · the same entry in another collection · chain B against B, 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 Q89YR8
- Elsewhere: RCSB PDB 4A2L · PDBe 4A2L · UniProt Q89YR8
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