Research workbench
Crystal structure of E. COLI mccb + succinimide
Analyse Crystal structure of E. COLI mccb + succinimide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H5R
- Type
- protein
- Length
- 1,364 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mccb protein; Microcin C7 analog
- UniProt
- Q47506, Q47505
- Ligands
- SNN, ZN, SO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mccb protein | protein | 340 | 39% helix, 19% strand | Q47506 |
| B | Mccb protein | protein | 334 | 41% helix, 19% strand | Q47506 |
| C | Mccb protein | protein | 343 | 40% helix, 20% strand | Q47506 |
| D | Mccb protein | protein | 333 | 40% helix, 20% strand | Q47506 |
| E, F | Microcin C7 analog | protein | 6 | 0% helix, 0% strand | Q47505 |
| G, H | Microcin C7 analog | protein | 1 | 0% helix, 0% strand | Q47505 |
Ligands and binding sites
- SNN · L-3-aminosuccinimide · ligand · 2 copies · chains A, E, B, F
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.74 | 0.79 | 86 | empty |
| 2 | 860 | 0.74 | 0.78 | 90 | empty |
| 3 | 503 | 0.71 | 0.81 | 62 | empty |
| 4 | 430 | 0.65 | 0.78 | 61 | SNN |
| 5 | 473 | 0.61 | 0.75 | 60 | SNN |
Interfaces
12 interfaces between chains.
- A–B · 4244 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 4216 Ų buried · 48 hydrogen bonds · protein-protein
- A–E · 436 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 431 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 414 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3H5R · Crystal structure of E. coli MccB + Succinimide · 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 Q47506
- Every structure of UniProt Q47505
- Elsewhere: RCSB PDB 3H5R · PDBe 3H5R · UniProt Q47506 · UniProt Q47505
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