MolNFT v1 · #88881 · protein
Chlamydia trachomatis nrdb with a MN/FE cofactor (procedure 2 - low mn)
4D8G · Ribonucleoside-diphosphate reductase subunit beta: “Chlamydia trachomatis nrdb with a MN/FE cofactor (procedure 2 - low mn)”. X-ray diffraction, 2 ligands (MN, FE), 7 pockets (best druggability 0.74). MolNFT v1 #88881 on GenesisL1…
- PDB
- 4D8G
- Type
- protein
- Length
- 1,315 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase subunit beta
- EC
- 1.17.4.1
- UniProt
- O84835
- Ligands
- MN, FE
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 326 | 69% helix, 1% strand | O84835 |
| B | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 334 | 69% helix, 1% strand | O84835 |
| C | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 324 | 70% helix, 1% strand | O84835 |
| D | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 331 | 70% helix, 1% strand | O84835 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.74 | 0.83 | 40 | empty |
| 2 | 989 | 0.71 | 0.75 | 96 | empty |
| 3 | 628 | 0.71 | 0.79 | 64 | empty |
| 4 | 623 | 0.69 | 0.77 | 64 | empty |
| 5 | 336 | 0.59 | 0.77 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3678 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 3363 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 418 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 382 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4D8G · Chlamydia trachomatis NrdB with a Mn/Fe cofactor (procedure 2 - low Mn) · the same entry in another collection · chain D against D, TM-score 1.00
- O84835 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase subunit beta… · a predicted model of the same protein · chain D 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 O84835
- Elsewhere: RCSB PDB 4D8G · PDBe 4D8G · UniProt O84835
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