Research workbench
Cryoem structure of modular pks holo-LSD14 bound to antibody fragment 1B2, composite structure
Analyse Cryoem structure of modular pks holo-LSD14 bound to antibody fragment 1B2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S6D
- Type
- protein
- Length
- 3,112 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-deoxyerythronolide-B synthase ERYA2, modules 3 and 4, LSD14 polyketide synthase fusion…
- EC
- 2.3.1.94
- UniProt
- B6ZK67, Q03132
- Ligands
- ATR
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 6-deoxyerythronolide-B synthase ERYA2, modules 3 and 4, LSD14 polyketide synthase fusion (EC 2.3.1.94) | protein | 478 | 41% helix, 21% strand | B6ZK67 |
| A | 6-deoxyerythronolide-B synthase ERYA2, modules 3 and 4, LSD14 polyketide synthase fusion (EC 2.3.1.94) | protein | 895 | 40% helix, 18% strand | Q03132, B6ZK67 |
| B | 6-deoxyerythronolide-B synthase ERYA2, modules 3 and 4, LSD14 polyketide synthase fusion (EC 2.3.1.94) | protein | 893 | 40% helix, 18% strand | Q03132, B6ZK67 |
| E | Fab 1B2 heavy chain | protein | 207 | 3% helix, 48% strand | — |
| G | Fab 1B2 light chain | protein | 214 | 6% helix, 43% strand | — |
| D | Fab 1B2 heavy chain | protein | 208 | 6% helix, 49% strand | — |
| F | Fab 1B2 light chain | protein | 217 | 6% helix, 38% strand | — |
Ligands and binding sites
- ATR · 2'-monophosphoadenosine-5'-diphosphate · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.81 | 0.84 | 68 | empty |
| 2 | 630 | 0.79 | 0.84 | 64 | empty |
| 3 | 1192 | 0.77 | 0.79 | 109 | empty |
| 4 | 541 | 0.76 | 0.83 | 59 | empty |
| 5 | 99 | 0.74 | 0.96 | 25 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2789 Ų buried · 17 hydrogen bonds · protein-protein
- E–G · 1563 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1539 Ų buried · 8 hydrogen bonds · protein-protein
- C–A · 770 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 609 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7S6D · CryoEM structure of modular PKS holo-Lsd14 bound to antibody fragment 1B2, composite… · 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 B6ZK67
- Every structure of UniProt Q03132
- Elsewhere: RCSB PDB 7S6D · PDBe 7S6D · UniProt B6ZK67 · UniProt Q03132
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