Research workbench
Crystal structure of translation elongation factor selb from methanococcus maripaludis in complex with GDP
Analyse Crystal structure of translation elongation factor selb from methanococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AC9
- Type
- protein
- Length
- 1,842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MJ0495-like protein
- UniProt
- Q8J307
- Ligands
- DXC, GDP, 5GP, MG, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MJ0495-like protein | protein | 448 | 17% helix, 44% strand | Q8J307 |
| B | MJ0495-like protein | protein | 456 | 17% helix, 44% strand | Q8J307 |
| C | MJ0495-like protein | protein | 471 | 18% helix, 44% strand | Q8J307 |
| D | MJ0495-like protein | protein | 467 | 14% helix, 43% strand | Q8J307 |
Ligands and binding sites
- DXC · (3alpha,5beta,12alpha)-3,12-dihydroxycholan-24-oic acid · ligand · 7 copies · chains B, C
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- 5GP · Guanosine-5'-monophosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 7 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.77 | 0.81 | 63 | 5GP |
| 2 | 752 | 0.71 | 0.77 | 92 | SO4, MG, DXC |
| 3 | 62 | 0.67 | 0.95 | 22 | empty |
| 4 | 191 | 0.64 | 0.85 | 32 | empty |
| 5 | 355 | 0.64 | 0.79 | 44 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1250 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 883 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 574 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (nonstandard).
Compared structures
- 4AC9 · Crystal structure of translation elongation factor selb from methanococcus maripaludis in… · 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 Q8J307
- Elsewhere: RCSB PDB 4AC9 · PDBe 4AC9 · UniProt Q8J307
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