MolNFT v1 · #77270 · protein
Structure of ECHA1_1 from mycobacterium paratuberculosis atcc baa-968 / K-10
3R9T: “Structure of ECHA1_1 from mycobacterium paratuberculosis atcc baa-968 / K-10”. X-ray diffraction, 1 ligand (BEZ), 7 pockets (best druggability 0.83). MolNFT v1 #77270 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3R9T
- Type
- protein
- Length
- 781 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ECHA1_1
- EC
- 4.2.1.17
- UniProt
- Q73WL5
- Ligands
- BEZ
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ECHA1_1 (EC 4.2.1.17) | protein | 260 | 45% helix, 18% strand | Q73WL5 |
| B | ECHA1_1 (EC 4.2.1.17) | protein | 262 | 45% helix, 18% strand | Q73WL5 |
| C | ECHA1_1 (EC 4.2.1.17) | protein | 259 | 45% helix, 19% strand | Q73WL5 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.83 | 0.85 | 117 | empty |
| 2 | 591 | 0.72 | 0.80 | 54 | BEZ |
| 3 | 472 | 0.72 | 0.81 | 40 | BEZ |
| 4 | 500 | 0.68 | 0.78 | 46 | BEZ |
| 5 | 79 | 0.38 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1412 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1370 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1337 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3R9T · Structure of EchA1_1 from Mycobacterium paratuberculosis ATCC BAA-968 / K-10 · 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 Q73WL5
- Elsewhere: RCSB PDB 3R9T · PDBe 3R9T · UniProt Q73WL5
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