Research workbench
X-ray crystal structure of chlamydia trachomatis apo nrdb
Analyse X-ray crystal structure of chlamydia trachomatis apo nrdb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M1H
- Type
- protein
- Length
- 1,332 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
- Pockets
- 13 · best druggability 0.77
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 | 331 | 70% helix, 1% strand | O84835 |
| B | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 336 | 69% helix, 1% strand | O84835 |
| C | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 331 | 70% helix, 1% strand | O84835 |
| D | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 334 | 69% helix, 1% strand | O84835 |
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.77 | 0.81 | 76 | empty |
| 2 | 663 | 0.71 | 0.78 | 68 | empty |
| 3 | 227 | 0.58 | 0.79 | 23 | empty |
| 4 | 236 | 0.57 | 0.79 | 31 | empty |
| 5 | 81 | 0.49 | 0.83 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3586 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3379 Ų buried · 50 hydrogen bonds · protein-protein
- B–D · 460 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 386 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4M1H · X-ray crystal structure of Chlamydia trachomatis apo NrdB · 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 C 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 4M1H · PDBe 4M1H · UniProt O84835
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