Research workbench
Crosslinked ACPP=FABZ complex from E. COLI type II fas
Analyse Crosslinked ACPP=FABZ complex from E. COLI type II fas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N3P
- Type
- protein
- Length
- 1,314 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz; Acyl carrier protein
- EC
- 4.2.1.59
- UniProt
- B7MBG1, B7MJ81
- Ligands
- XLN
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 11 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 144 | 21% helix, 42% strand | B7MBG1 |
| B | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 145 | 21% helix, 42% strand | B7MBG1 |
| C | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 144 | 21% helix, 41% strand | B7MBG1 |
| D | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 146 | 21% helix, 42% strand | B7MBG1 |
| E, F | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 146 | 21% helix, 42% strand | B7MBG1 |
| G | Acyl carrier protein | protein | 72 | 57% helix, 3% strand | B7MJ81 |
| H | Acyl carrier protein | protein | 75 | 56% helix, 3% strand | B7MJ81 |
| I | Acyl carrier protein | protein | 76 | 51% helix, 3% strand | B7MJ81 |
| J | Acyl carrier protein | protein | 73 | 56% helix, 3% strand | B7MJ81 |
| K | Acyl carrier protein | protein | 77 | 55% helix, 3% strand | B7MJ81 |
| L | Acyl carrier protein | protein | 70 | 54% helix, 3% strand | B7MJ81 |
Ligands and binding sites
- XLN · N~3~-{(2R)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-(3-{[(1Z)-pent-1-en-1-yl]sulfonyl}propyl)-beta-alaninamide · ligand · 6 copies · chains A, B, I, K, C, D, L, H, E, F, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.86 | 0.94 | 54 | empty |
| 2 | 256 | 0.74 | 0.88 | 42 | XLN |
| 3 | 257 | 0.74 | 0.88 | 35 | XLN |
| 4 | 376 | 0.73 | 0.84 | 59 | XLN |
| 5 | 719 | 0.72 | 0.78 | 54 | empty |
Interfaces
25 interfaces between chains.
- A–B · 1448 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1406 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1403 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1246 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 1242 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 6N3P · Crosslinked AcpP=FabZ complex from E. coli Type II FAS · the same entry in another collection · chain L against L, 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 B7MBG1
- Every structure of UniProt B7MJ81
- Elsewhere: RCSB PDB 6N3P · PDBe 6N3P · UniProt B7MBG1 · UniProt B7MJ81
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