MolNFT v1 · #181832 · protein
6-deoxyerythronolide B synthase (debs) module 1 in complex with antibody fragment 1B2: "turnstile closed" state (te-free)
7M7J · Eryai: “6-deoxyerythronolide B synthase (debs) module 1 in complex with antibody fragment 1B2: "turnstile closed"…”. Electron microscopy, 20 pockets (best druggability 0.78). MolNFT v1 #181832 on GenesisL1: 3D structure, binding…
- PDB
- 7M7J
- Type
- protein
- Length
- 3,124 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eryai; 1B2 (heavy chain); 1B2 (light chain)
- UniProt
- Q5UNP6
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 28% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Eryai | protein | 912 | 35% helix, 13% strand | Q5UNP6 |
| A | Eryai | protein | 1390 | 35% helix, 14% strand | Q5UNP6 |
| C, E | 1B2 (heavy chain) | protein | 205 | 3% helix, 46% strand | — |
| D | 1B2 (light chain) | protein | 206 | 3% helix, 34% strand | — |
| F | 1B2 (light chain) | protein | 206 | 4% helix, 33% strand | — |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.78 | 0.80 | 116 | empty |
| 2 | 123 | 0.77 | 0.96 | 37 | empty |
| 3 | 362 | 0.75 | 0.86 | 64 | empty |
| 4 | 599 | 0.74 | 0.81 | 74 | empty |
| 5 | 453 | 0.71 | 0.81 | 42 | empty |
Interfaces
11 interfaces between chains.
- B–A · 4804 Ų buried · 83 hydrogen bonds · protein-protein
- E–F · 1592 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1573 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 922 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 863 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7M7J · 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 7M7J · PDBe 7M7J · UniProt Q5UNP6
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