Research workbench
Crystal structure of SPT4/5NGN heterodimer complex from methanococcus jannaschii
Analyse Crystal structure of SPT4/5NGN heterodimer complex from methanococcus jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LPE
- Type
- protein
- Length
- 572 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative transcription antitermination protein nusg; DNA-directed RNA polymerase subunit…
- EC
- 2.7.7.6
- UniProt
- Q57818, Q57839
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Putative transcription antitermination protein nusg | protein | 84 | 36% helix, 26% strand | Q57818 |
| B, D, F, H | DNA-directed RNA polymerase subunit E'' (EC 2.7.7.6) | protein | 59 | 8% helix, 36% strand | Q57839 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.66 | 0.79 | 33 | empty |
| 2 | 322 | 0.56 | 0.75 | 32 | empty |
| 3 | 275 | 0.52 | 0.75 | 32 | empty |
| 4 | 74 | 0.31 | 0.74 | 16 | empty |
Interfaces
9 interfaces between chains.
- G–H · 982 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 978 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 974 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 970 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 497 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3LPE · Crystal structure of Spt4/5NGN heterodimer complex from Methanococcus jannaschii · the same entry in another collection · chain H against H, TM-score 1.00
- Q57839 · AlphaFold monomer V2.0 prediction for transcription elongation factor SPT4 (Q57839) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q57818 · AlphaFold monomer V2.0 prediction for transcription elongation factor SPT5 (Q57818) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q57818
- Every structure of UniProt Q57839
- Elsewhere: RCSB PDB 3LPE · PDBe 3LPE · UniProt Q57818 · UniProt Q57839
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