Research workbench
Holocomplex of E. COLI class ia ribonucleotide reductase with GDP and ttp
Analyse Holocomplex of E. COLI class ia ribonucleotide reductase with GDP and ttp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W4X
- Type
- protein
- Length
- 2,190 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase 1 subunit alpha; Ribonucleoside-diphosphate…
- EC
- 1.17.4.1
- UniProt
- P00452, P69924
- Ligands
- TTP, FEO, GDP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 736 | 42% helix, 9% strand | P00452 |
| B | Ribonucleoside-diphosphate reductase 1 subunit alpha (EC 1.17.4.1) | protein | 738 | 44% helix, 12% strand | P00452 |
| C | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 375 | 63% helix, 5% strand | P69924 |
| D | Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) | protein | 341 | 68% helix, 1% strand | P69924 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B
- FEO · Mu-oxo-diiron · ligand · 2 copies · chains C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B, C
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.86 | 0.87 | 117 | empty |
| 2 | 441 | 0.83 | 0.91 | 73 | TTP, GDP |
| 3 | 158 | 0.81 | 0.97 | 44 | empty |
| 4 | 990 | 0.80 | 0.82 | 93 | TTP |
| 5 | 412 | 0.76 | 0.86 | 53 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3548 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 3473 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 1465 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 541 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 225 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified, 1 disulfide (nonstandard, disulfide).
Compared structures
- 6W4X · Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP · the same entry in another collection · chain A against A, TM-score 1.00
- P00452 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase 1 subunit… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P00452
- Every structure of UniProt P69924
- Elsewhere: RCSB PDB 6W4X · PDBe 6W4X · UniProt P00452 · UniProt P69924
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