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Crystal structure of the N-fopmylmaleamic acid deformylase NFO(S94A) from pseudomonas putida S16
Analyse Crystal structure of the N-fopmylmaleamic acid deformylase NFO(S94A) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L0C
- Type
- protein
- Length
- 2,029 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deformylase
- UniProt
- F8G0M2
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Deformylase | protein | 255 | 43% helix, 19% strand | F8G0M2 |
| C, D | Deformylase | protein | 253 | 43% helix, 19% strand | F8G0M2 |
| F | Deformylase | protein | 252 | 43% helix, 19% strand | F8G0M2 |
| G | Deformylase | protein | 252 | 42% helix, 19% strand | F8G0M2 |
| H | Deformylase | protein | 254 | 43% helix, 19% strand | F8G0M2 |
Ligands and binding sites
- ACY · Acetic acid · additive · 10 copies · chains A, B, C, D, E, F, G, H
- PEG · Di(hydroxyethyl)ether · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.77 | 0.79 | 104 | empty |
| 2 | 761 | 0.71 | 0.77 | 74 | empty |
| 3 | 368 | 0.63 | 0.78 | 31 | ACY |
| 4 | 227 | 0.58 | 0.79 | 31 | ACY, PEG |
| 5 | 212 | 0.57 | 0.79 | 30 | ACY |
Interfaces
10 interfaces between chains.
- A–G · 849 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 845 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 697 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 641 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 259 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 modified (engineered).
Compared structures
- 4L0C · Crystal structure of the N-Fopmylmaleamic acid deformylase Nfo(S94A) from Pseudomonas… · the same entry in another collection · chain B against B, 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 F8G0M2
- Elsewhere: RCSB PDB 4L0C · PDBe 4L0C · UniProt F8G0M2
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