MolNFT v1 · #15384 · protein + RNA
LAMBDA3 elongation complex with four phosphodiester bond formed
1N35 · 5'-R(P*GP*GP*GP*GP*G)-3': “LAMBDA3 elongation complex with four phosphodiester bond formed”. X-ray diffraction, 2 ligands (CH1, MN), 16 pockets (best druggability 0.86). MolNFT v1 #15384 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1N35
- Type
- protein + RNA
- Length
- 1,277 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*GP*GP*GP*GP*G)-3'; 5'-R(*AP*UP*UP*AP*GP*CP*CP*CP*CP*C)-3'; Minor core protein…
- UniProt
- P17378
- Ligands
- CH1, MN
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(P*GP*GP*GP*GP*G)-3' | rna | 5 | — | — |
| C | 5'-R(*AP*UP*UP*AP*GP*CP*CP*CP*CP*C)-3' | rna | 8 | — | — |
| A | Minor core protein lambda 3 | protein | 1264 | 48% helix, 13% strand | P17378 |
Ligands and binding sites
- CH1 · 3'-deoxy-cytidine-5'-triphosphate · ligand · 3 copies · chains B, C, A
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.86 | 0.89 | 112 | MN, CH1 |
| 2 | 92 | 0.75 | 0.96 | 27 | empty |
| 3 | 517 | 0.74 | 0.82 | 59 | empty |
| 4 | 137 | 0.64 | 0.87 | 30 | empty |
| 5 | 407 | 0.61 | 0.76 | 42 | CH1 |
Interfaces
3 interfaces between chains.
- C–A · 1070 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–A · 671 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 256 Ų buried · 14 hydrogen bonds · nucleic-nucleic
Compared structures
- 1N35 · lambda3 elongation complex with four phosphodiester bond formed · the same entry in another collection · chain B against B, 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 P17378
- Elsewhere: RCSB PDB 1N35 · PDBe 1N35 · UniProt P17378
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