Research workbench
Crystal structure of EIS2 from mycobacterium abscessus
Analyse Crystal structure of EIS2 from mycobacterium abscessus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RFX
- Type
- protein
- Length
- 2,424 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EIS2
- EC
- 2.3.1.-
- UniProt
- A0A3A1BNP8
- Ligands
- P4K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | EIS2 (EC 2.3.1.-) | protein | 401 | 32% helix, 33% strand | A0A3A1BNP8 |
| A | EIS2 (EC 2.3.1.-) | protein | 404 | 32% helix, 33% strand | A0A3A1BNP8 |
| B | EIS2 (EC 2.3.1.-) | protein | 404 | 32% helix, 33% strand | A0A3A1BNP8 |
| C | EIS2 (EC 2.3.1.-) | protein | 403 | 32% helix, 32% strand | A0A3A1BNP8 |
| E, F | EIS2 (EC 2.3.1.-) | protein | 406 | 31% helix, 32% strand | A0A3A1BNP8 |
Ligands and binding sites
- P4K · polyethylene glycol · ligand · 7 copies · chains D, A, B, C, E
- CIT · Citric acid · additive · 6 copies · chains D, A, B, C, E, F
- ACT · Acetate ion · additive · 5 copies · chains D, A, B, C, E
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 | 410 | 0.85 | 0.93 | 47 | empty |
| 2 | 402 | 0.84 | 0.93 | 47 | P4K |
| 3 | 395 | 0.83 | 0.92 | 48 | P4K |
| 4 | 1171 | 0.83 | 0.84 | 108 | P4K |
| 5 | 1014 | 0.81 | 0.82 | 97 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1946 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1909 Ų buried · 18 hydrogen bonds · protein-protein
- D–A · 1861 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 650 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 6RFX · Crystal structure of Eis2 from Mycobacterium abscessus · the same entry in another collection · chain D against D, 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 A0A3A1BNP8
- Elsewhere: RCSB PDB 6RFX · PDBe 6RFX · UniProt A0A3A1BNP8
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