Research workbench
Fic protein from neisseria meningitidis mutant DELTA8 in complex with amppnp
Analyse Fic protein from neisseria meningitidis mutant DELTA8 in complex with amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SE5
- Type
- protein
- Length
- 620 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell filamentation protein fic-related protein
- UniProt
- Q7DDR9
- Ligands
- ANP, MG
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cell filamentation protein fic-related protein | protein | 155 | 58% helix, 6% strand | Q7DDR9 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.83 | 0.84 | 108 | ANP, MG |
| 2 | 170 | 0.45 | 0.74 | 26 | empty |
| 3 | 174 | 0.44 | 0.74 | 24 | empty |
| 4 | 163 | 0.42 | 0.74 | 24 | empty |
| 5 | 123 | 0.39 | 0.74 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–C · 864 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 862 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 411 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 400 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 187 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3SE5 · Fic protein from NEISSERIA MENINGITIDIS mutant delta8 in complex with AMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
- Q7DDR9 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase nmfic (Q7DDR9) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q7DDR9
- Elsewhere: RCSB PDB 3SE5 · PDBe 3SE5 · UniProt Q7DDR9
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