Research workbench
Structure of E. COLI MS115-1 CDNC:HORMA-deltan complex
Analyse Structure of E. COLI MS115-1 CDNC:HORMA-deltan complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U7B
- Type
- protein
- Length
- 986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E. COLI MS115-1 cdnc; BACHORMA_1 domain-containing protein
- UniProt
- D7Y2H2, A0A1X1LKT4
- Ligands
- AMP, MG, CL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E. COLI MS115-1 cdnc | protein | 315 | 52% helix, 12% strand | D7Y2H2 |
| B | BACHORMA_1 domain-containing protein | protein | 176 | 31% helix, 34% strand | A0A1X1LKT4 |
| C | E. COLI MS115-1 cdnc | protein | 320 | 50% helix, 13% strand | D7Y2H2 |
| D | BACHORMA_1 domain-containing protein | protein | 175 | 29% helix, 34% strand | A0A1X1LKT4 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
- ACT · Acetate ion · additive · 5 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.79 | 0.81 | 108 | ACT |
| 2 | 634 | 0.74 | 0.81 | 46 | MG, AMP |
| 3 | 674 | 0.70 | 0.77 | 56 | MG |
| 4 | 171 | 0.42 | 0.74 | 20 | ACT |
| 5 | 134 | 0.39 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1994 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 780 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 754 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 D7Y2H2
- Every structure of UniProt A0A1X1LKT4
- Elsewhere: RCSB PDB 6U7B · PDBe 6U7B · UniProt D7Y2H2 · UniProt A0A1X1LKT4
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