Research workbench
Crystal structure of fabg from plesiocystis pacifica
Analyse Crystal structure of fabg from plesiocystis pacifica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NBW
- Type
- protein
- Length
- 1,012 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- A6G411
- Ligands
- NAD
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 253 | 49% helix, 20% strand | A6G411 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.84 | 0.85 | 79 | empty |
| 2 | 555 | 0.72 | 0.80 | 49 | NAD |
| 3 | 593 | 0.71 | 0.79 | 56 | NAD |
| 4 | 473 | 0.71 | 0.81 | 50 | NAD |
| 5 | 615 | 0.71 | 0.79 | 62 | NAD |
Interfaces
6 interfaces between chains.
- A–C · 2013 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 2005 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1276 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1275 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 336 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4NBW · Crystal structure of FabG from Plesiocystis pacifica · 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 A6G411
- Elsewhere: RCSB PDB 4NBW · PDBe 4NBW · UniProt A6G411
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