MolNFT v1 · #13113 · protein
Crystal structure of B-12 dependent (class II) ribonucleotide reductase
1L1L · Ribonucleoside triphosphate reductase: “Crystal structure of B-12 dependent (class II) ribonucleotide reductase”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #13113 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1L1L
- Type
- protein
- Length
- 2,868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside triphosphate reductase
- EC
- 1.17.4.2
- UniProt
- Q59490
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribonucleoside triphosphate reductase (EC 1.17.4.2) | protein | 717 | 41% helix, 18% strand | Q59490 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.79 | 0.80 | 135 | empty |
| 2 | 723 | 0.75 | 0.80 | 91 | empty |
| 3 | 525 | 0.71 | 0.80 | 71 | empty |
| 4 | 859 | 0.71 | 0.77 | 107 | empty |
| 5 | 363 | 0.67 | 0.80 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–B · 911 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 521 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 432 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 93 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 43 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1L1L · Crystal structure of B-12 dependent (class II) ribonucleotide reductase · the same entry in another collection · chain A against A, TM-score 1.00
- Q59490 · AlphaFold monomer V2.0 prediction for adenosylcobalamin-dependent… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q59490
- Elsewhere: RCSB PDB 1L1L · PDBe 1L1L · UniProt Q59490
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