MolNFT v1 · #85119 · protein
Structure of the periplasmic domain of the heparin and heparan sulphate sensing hybrid two component system BT4663 in apo and ligand bound forms
4A2L · 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, 1 ligand (OAA), 20 pockets (best druggability…
- 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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