MolNFT v1 · #85434 · protein
Crystal structure of translation elongation factor selb from methanococcus maripaludis in complex with the GTP analogue gppnhp
4ACB: “Crystal structure of translation elongation factor selb from methanococcus maripaludis in complex with the…”. X-ray diffraction, 6 ligands (DXC, GNP, GDP), 20 pockets (best druggability 0.77). MolNFT v1 #85434 on GenesisL1: 3D…
- PDB
- 4ACB
- Type
- protein
- Length
- 1,846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation elongation factor selb
- UniProt
- Q8J307
- Ligands
- DXC, GNP, 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 | Translation elongation factor selb | protein | 452 | 15% helix, 45% strand | Q8J307 |
| B | Translation elongation factor selb | protein | 456 | 17% helix, 43% strand | Q8J307 |
| C | Translation elongation factor selb | protein | 471 | 17% helix, 44% strand | Q8J307 |
| D | Translation elongation factor selb | protein | 467 | 14% helix, 44% strand | Q8J307 |
Ligands and binding sites
- DXC · (3alpha,5beta,12alpha)-3,12-dihydroxycholan-24-oic acid · ligand · 7 copies · chains B, C
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- 5GP · Guanosine-5'-monophosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.77 | 0.80 | 79 | 5GP |
| 2 | 88 | 0.72 | 0.95 | 25 | empty |
| 3 | 661 | 0.70 | 0.78 | 81 | SO4 |
| 4 | 390 | 0.68 | 0.81 | 43 | empty |
| 5 | 403 | 0.67 | 0.80 | 44 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1251 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 892 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 572 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (nonstandard).
Compared structures
- 4ACB · 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 4ACB · PDBe 4ACB · UniProt Q8J307
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