Research workbench
Chlamydia trachomatis nrdb with a MN/FE cofactor (procedure 1 - high mn)
Analyse Chlamydia trachomatis nrdb with a MN/FE cofactor (procedure 1 - high mn) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D8F
- 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
- FE, MN
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 327 | 71% helix, 1% strand | O84835 |
| B | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 334 | 68% 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 | 330 | 71% helix, 1% strand | O84835 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.75 | 0.84 | 53 | empty |
| 2 | 1011 | 0.71 | 0.75 | 83 | empty |
| 3 | 655 | 0.70 | 0.78 | 66 | empty |
| 4 | 598 | 0.70 | 0.78 | 62 | empty |
| 5 | 418 | 0.62 | 0.76 | 47 | ACY |
Interfaces
4 interfaces between chains.
- A–B · 3583 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3386 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 451 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 330 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4D8F · Chlamydia trachomatis NrdB with a Mn/Fe cofactor (procedure 1 - high 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 4D8F · PDBe 4D8F · UniProt O84835
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