MolNFT v1 · #153465 · protein
Met-ala-ser bound crystal structure of class I type B peptide deformylase from pseudomonas aeruginosa
6JFA: “Met-ala-ser bound crystal structure of class I type B peptide deformylase from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (NI), 5 pockets (best druggability 0.59). MolNFT v1 #153465 on GenesisL1: 3D structure, binding…
- PDB
- 6JFA
- Type
- protein
- Length
- 321 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase; Met-ala-ser
- EC
- 3.5.1.88
- UniProt
- A0A1C7BES9
- Ligands
- NI
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 158 | 31% helix, 31% strand | A0A1C7BES9 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 160 | 33% helix, 33% strand | A0A1C7BES9 |
| C | Met-ala-ser | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.59 | 0.84 | 23 | empty |
| 2 | 168 | 0.58 | 0.82 | 27 | empty |
| 3 | 91 | 0.45 | 0.80 | 17 | NI |
| 4 | 68 | 0.31 | 0.74 | 19 | empty |
| 5 | 65 | 0.30 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 510 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 309 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6JFA · Met-Ala-Ser bound crystal structure of class I type b peptide deformylase from… · the same entry in another collection · chain A 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 A0A1C7BES9
- Elsewhere: RCSB PDB 6JFA · PDBe 6JFA · UniProt A0A1C7BES9
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