MolNFT v1 · #144962 · protein
Crystal structure of [KS3][AT3] didomain from module 3 of 6- deoxyerthronolide B synthase in complex with antibody fragment (Fab)
6C9U · 6-deoxyerythronolide-B synthase ERYA2, modules 3 and 4: “Crystal structure of [KS3][AT3] didomain from module 3 of 6- deoxyerthronolide B synthase in complex with…”. X-ray diffraction, 2 ligands (NA, K), 17 pockets (best…
- PDB
- 6C9U
- Type
- protein
- Length
- 1,311 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-deoxyerythronolide-B synthase ERYA2, modules 3 and 4; Light chain of Fab 1B2; Heavy…
- EC
- 2.3.1.94
- UniProt
- Q03132
- Ligands
- NA, K
- Pockets
- 17 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-deoxyerythronolide-B synthase ERYA2, modules 3 and 4 (EC 2.3.1.94) | protein | 897 | 41% helix, 17% strand | Q03132 |
| L | Light chain of Fab 1B2 | protein | 209 | 6% helix, 47% strand | — |
| H | Heavy chain of Fab 1B2 | protein | 205 | 6% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.65 | 0.80 | 49 | empty |
| 2 | 438 | 0.61 | 0.76 | 53 | empty |
| 3 | 401 | 0.59 | 0.75 | 44 | empty |
| 4 | 113 | 0.57 | 0.84 | 20 | empty |
| 5 | 102 | 0.54 | 0.84 | 21 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1592 Ų buried · 15 hydrogen bonds · protein-protein
- A–L · 453 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 modified (disulfide, oxidation).
Compared structures
- 6C9U · Crystal structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase… · 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 Q03132
- Elsewhere: RCSB PDB 6C9U · PDBe 6C9U · UniProt Q03132
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