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Crystallographic structure of the enzymatically active N-terminal domain of the rel protein from mycobacterium tuberculosis
Analyse Crystallographic structure of the enzymatically active N-terminal domain of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XNX
- Type
- protein
- Length
- 1,276 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional (P)PPGPP SYNTHASE/HYDROLASE rela
- EC
- 2.7.6.5, 3.1.7.2
- UniProt
- P9WHG9
- Ligands
- MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional (P)PPGPP SYNTHASE/HYDROLASE rela (EC 2.7.6.5, 3.1.7.2) | protein | 323 | 61% helix, 8% strand | P9WHG9 |
| B | Bifunctional (P)PPGPP SYNTHASE/HYDROLASE rela (EC 2.7.6.5, 3.1.7.2) | protein | 316 | 58% helix, 7% strand | P9WHG9 |
| C | Bifunctional (P)PPGPP SYNTHASE/HYDROLASE rela (EC 2.7.6.5, 3.1.7.2) | protein | 316 | 60% helix, 8% strand | P9WHG9 |
| D | Bifunctional (P)PPGPP SYNTHASE/HYDROLASE rela (EC 2.7.6.5, 3.1.7.2) | protein | 321 | 61% helix, 8% strand | P9WHG9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.78 | 0.80 | 114 | empty |
| 2 | 646 | 0.76 | 0.81 | 72 | empty |
| 3 | 569 | 0.75 | 0.82 | 63 | empty |
| 4 | 763 | 0.71 | 0.78 | 82 | empty |
| 5 | 120 | 0.71 | 0.92 | 40 | empty |
Interfaces
4 interfaces between chains.
- B–C · 847 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 317 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 200 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XNX · Crystallographic structure of the enzymatically active N-terminal domain of the Rel… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WHG9 · AlphaFold monomer V2.0 prediction for bifunctional (P)PPGPP SYNTHASE/HYDROLASE rela… · a predicted model of the same protein · chain C against A, TM-score 0.92
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 P9WHG9
- Elsewhere: RCSB PDB 5XNX · PDBe 5XNX · UniProt P9WHG9
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