Research workbench
Crystal structure of mycobacterium tuberculosis reljk (RV3357-RV3358- RELBE3)
Analyse Crystal structure of mycobacterium tuberculosis reljk (RV3357-RV3358- RELBE3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OEI
- Type
- protein
- Length
- 1,356 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Relj (antitoxin RV3357); Relk (toxin RV3358)
- EC
- 3.1.-.-
- UniProt
- P65067, P64528
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 10 distinct chains · 56% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Relj (antitoxin RV3357) | protein | 87 | 62% helix, 16% strand | P65067 |
| B | Relj (antitoxin RV3357) | protein | 91 | 59% helix, 15% strand | P65067 |
| C, D, H | Relk (toxin RV3358) (EC 3.1.-.-) | protein | 85 | 38% helix, 26% strand | P64528 |
| E | Relj (antitoxin RV3357) | protein | 82 | 66% helix, 16% strand | P65067 |
| F, J | Relj (antitoxin RV3357) | protein | 86 | 63% helix, 16% strand | P65067 |
| G, O | Relk (toxin RV3358) (EC 3.1.-.-) | protein | 83 | 39% helix, 24% strand | P64528 |
| I | Relj (antitoxin RV3357) | protein | 83 | 66% helix, 16% strand | P65067 |
| K, L, P | Relk (toxin RV3358) (EC 3.1.-.-) | protein | 84 | 38% helix, 26% strand | P64528 |
| M | Relj (antitoxin RV3357) | protein | 85 | 65% helix, 15% strand | P65067 |
| N | Relj (antitoxin RV3357) | protein | 83 | 61% helix, 17% strand | P65067 |
Ligands and binding sites
- FLC · Citrate anion · additive · chains C, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.72 | 0.76 | 92 | empty |
| 2 | 817 | 0.66 | 0.74 | 89 | FLC |
| 3 | 113 | 0.43 | 0.77 | 27 | empty |
| 4 | 101 | 0.41 | 0.77 | 23 | empty |
| 5 | 97 | 0.39 | 0.76 | 22 | empty |
Interfaces
39 interfaces between chains.
- B–D · 1856 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1742 Ų buried · 28 hydrogen bonds · protein-protein
- F–H · 1680 Ų buried · 26 hydrogen bonds · protein-protein
- J–L · 1670 Ų buried · 23 hydrogen bonds · protein-protein
- M–O · 1647 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 3OEI · Crystal structure of Mycobacterium tuberculosis RelJK (Rv3357-Rv3358-RelBE3) · 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 P65067
- Every structure of UniProt P64528
- Elsewhere: RCSB PDB 3OEI · PDBe 3OEI · UniProt P65067 · UniProt P64528
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