Research workbench
6-deoxyerythronolide B synthase (debs) module 1 in complex with antibody fragment 1B2: state 1
Analyse 6-deoxyerythronolide B synthase (debs) module 1 in complex with antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M7F
- Type
- protein
- Length
- 3,211 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ERYAI,6-deoxyerythronolide-B synthase ERYA3, modules 5 and 6 chimera; 1B2 (heavy chain)…
- EC
- 2.3.1.94
- UniProt
- Q5UNP6
- Ligands
- PN7
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 26% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | ERYAI,6-deoxyerythronolide-B synthase ERYA3, modules 5 and 6 chimera (EC 2.3.1.94) | protein | 999 | 35% helix, 14% strand | Q5UNP6 |
| A | ERYAI,6-deoxyerythronolide-B synthase ERYA3, modules 5 and 6 chimera (EC 2.3.1.94) | protein | 1390 | 29% helix, 15% strand | Q5UNP6 |
| C, E | 1B2 (heavy chain) | protein | 205 | 3% helix, 43% strand | — |
| D | 1B2 (light chain) | protein | 206 | 4% helix, 39% strand | — |
| F | 1B2 (light chain) | protein | 206 | 3% helix, 39% strand | — |
Ligands and binding sites
- PN7 · N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide · ligand · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.78 | 0.97 | 36 | empty |
| 2 | 1014 | 0.77 | 0.79 | 125 | PN7 |
| 3 | 85 | 0.76 | 0.98 | 38 | empty |
| 4 | 687 | 0.69 | 0.77 | 61 | empty |
| 5 | 125 | 0.63 | 0.87 | 31 | empty |
Interfaces
11 interfaces between chains.
- B–A · 4783 Ų buried · 70 hydrogen bonds · protein-protein
- C–D · 1673 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1669 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 900 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 794 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7M7F · 6-Deoxyerythronolide B synthase (DEBS) module 1 in complex with antibody fragment 1B2… · the same entry in another collection · chain B against B, 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 Q5UNP6
- Elsewhere: RCSB PDB 7M7F · PDBe 7M7F · UniProt Q5UNP6
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