MolNFT v1 · #85120 · protein
Structure of the periplasmic domain of the heparin and heparan sulphate sensing hybrid two component system BT4663 in apo and ligand bound forms
4A2M · Two-component system sensor histidine KINASE/RESPONSE: “Structure of the periplasmic domain of the heparin and heparan sulphate sensing hybrid two component system…”. X-ray diffraction, 2 ligands (NGS, GCD), 20 pockets (best…
- PDB
- 4A2M
- Type
- protein
- Length
- 2,979 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Two-component system sensor histidine KINASE/RESPONSE
- UniProt
- Q89YR8
- Ligands
- NGS, GCD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Two-component system sensor histidine KINASE/RESPONSE | protein | 741 | 2% helix, 47% strand | Q89YR8 |
| B | Two-component system sensor histidine KINASE/RESPONSE | protein | 750 | 2% helix, 46% strand | Q89YR8 |
| C | Two-component system sensor histidine KINASE/RESPONSE | protein | 743 | 2% helix, 47% strand | Q89YR8 |
| D | Two-component system sensor histidine KINASE/RESPONSE | protein | 745 | 2% helix, 47% strand | Q89YR8 |
Ligands and binding sites
- NGS · 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose · ligand · 4 copies · chains A, B, C, D
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 4 copies · chains A, B, C, 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 | 943 | 0.84 | 0.85 | 91 | NGS, GCD |
| 2 | 1151 | 0.83 | 0.84 | 94 | NGS, GCD |
| 3 | 1175 | 0.83 | 0.84 | 96 | NGS, GCD |
| 4 | 1184 | 0.82 | 0.83 | 103 | NGS, GCD |
| 5 | 745 | 0.73 | 0.79 | 80 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2562 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2495 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 683 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 216 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4A2M · Structure of the periplasmic domain of the heparin and heparan sulphate sensing hybrid… · 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 Q89YR8
- Elsewhere: RCSB PDB 4A2M · PDBe 4A2M · UniProt Q89YR8
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