Research workbench
6-deoxyerythronolide B synthase (debs) module 1 in complex with antibody fragment 1B2: state 2
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
- 7M7G
- Type
- protein
- Length
- 3,557 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
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ERYAI,6-deoxyerythronolide-B synthase ERYA3, modules 5 and 6 chimera (EC 2.3.1.94) | protein | 1356 | 33% helix, 14% strand | Q5UNP6 |
| B | ERYAI,6-deoxyerythronolide-B synthase ERYA3, modules 5 and 6 chimera (EC 2.3.1.94) | protein | 1379 | 31% 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 | — |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.81 | 0.96 | 37 | empty |
| 2 | 120 | 0.80 | 0.98 | 31 | empty |
| 3 | 955 | 0.77 | 0.80 | 92 | empty |
| 4 | 80 | 0.75 | 0.98 | 28 | empty |
| 5 | 623 | 0.74 | 0.81 | 72 | empty |
Interfaces
11 interfaces between chains.
- A–B · 3960 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 1677 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1673 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 919 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 644 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7M7G · 6-Deoxyerythronolide B synthase (DEBS) module 1 in complex with antibody fragment 1B2… · 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 Q5UNP6
- Elsewhere: RCSB PDB 7M7G · PDBe 7M7G · UniProt Q5UNP6
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