MolNFT v1 · #71864 · protein
Crystal structure of methionine aminopeptidase from rickettsia prowazekii
3MR1: “Crystal structure of methionine aminopeptidase from rickettsia prowazekii”. X-ray diffraction, 4 ligands (MN, NA, PO4), 11 pockets (best druggability 0.77). MolNFT v1 #71864 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3MR1
- Type
- protein
- Length
- 995 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase
- EC
- 3.4.11.18
- UniProt
- Q9ZCD3
- Ligands
- MN, NA, PO4, CL
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Methionine aminopeptidase (EC 3.4.11.18) | protein | 249 | 29% helix, 28% strand | Q9ZCD3 |
| B | Methionine aminopeptidase (EC 3.4.11.18) | protein | 248 | 29% helix, 27% strand | Q9ZCD3 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.77 | 0.80 | 101 | CL |
| 2 | 496 | 0.70 | 0.80 | 59 | empty |
| 3 | 230 | 0.61 | 0.81 | 37 | CL |
| 4 | 123 | 0.61 | 0.86 | 21 | PO4 |
| 5 | 135 | 0.58 | 0.84 | 24 | PO4 |
Interfaces
4 interfaces between chains.
- C–D · 579 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 545 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 383 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 167 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3MR1 · Crystal structure of methionine aminopeptidase from Rickettsia prowazekii · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZCD3 · AlphaFold monomer V2.0 prediction for methionine aminopeptidase (Q9ZCD3) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q9ZCD3
- Elsewhere: RCSB PDB 3MR1 · PDBe 3MR1 · UniProt Q9ZCD3
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