MolNFT v1 · #99371 · protein
X-ray crystal structure of chlamydia trachomatis MN(II)FE(II)-nrdb
4M1I · Ribonucleoside-diphosphate reductase subunit beta: “X-ray crystal structure of chlamydia trachomatis MN(II)FE(II)-nrdb”. X-ray diffraction, 2 ligands (MN, FE), 11 pockets (best druggability 0.72). MolNFT v1 #99371 on GenesisL1: 3D…
- PDB
- 4M1I
- Type
- protein
- Length
- 1,325 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
- 11 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 333 | 71% helix, 1% strand | O84835 |
| B | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 329 | 71% helix, 1% strand | O84835 |
| D | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 330 | 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
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, C
- ACY · Acetic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.72 | 0.79 | 71 | empty |
| 2 | 595 | 0.68 | 0.78 | 68 | empty |
| 3 | 467 | 0.67 | 0.79 | 68 | empty |
| 4 | 463 | 0.66 | 0.78 | 51 | empty |
| 5 | 232 | 0.58 | 0.79 | 37 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3565 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 3378 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 437 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 357 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4M1I · X-ray crystal structure of Chlamydia trachomatis Mn(II)Fe(II)-NrdB · the same entry in another collection · chain A against A, 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 4M1I · PDBe 4M1I · UniProt O84835
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