Research workbench
The coordinates of the monomeric terminase complex in the presence of the ADP-BEF3
Analyse The coordinates of the monomeric terminase complex in the presence of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M5U
- Type
- protein
- Length
- 1,359 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tripartite terminase subunit 3; Tripartite terminase subunit 1; Tripartite terminase…
- EC
- 3.1.-.-
- UniProt
- P04295, P10212, B9VQG1
- Ligands
- ADP, BEF, ZN, MG
- Pockets
- 16 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tripartite terminase subunit 3 (EC 3.1.-.-) | protein | 585 | 36% helix, 14% strand | P04295 |
| B | Tripartite terminase subunit 1 | protein | 670 | 54% helix, 3% strand | P10212 |
| C | Tripartite terminase subunit 2 | protein | 104 | 51% helix, 0% strand | B9VQG1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B, C
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.82 | 0.85 | 93 | ADP |
| 2 | 604 | 0.78 | 0.84 | 81 | empty |
| 3 | 866 | 0.76 | 0.80 | 70 | empty |
| 4 | 331 | 0.73 | 0.85 | 52 | empty |
| 5 | 50 | 0.69 | 0.98 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6339 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 4657 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 1057 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6M5U · The coordinates of the monomeric terminase complex in the presence of the ADP-BeF3 · 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 P04295
- Every structure of UniProt P10212
- Every structure of UniProt B9VQG1
- Elsewhere: RCSB PDB 6M5U · PDBe 6M5U · UniProt P04295 · UniProt P10212 · UniProt B9VQG1
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