Research workbench
Plasmid coupling protein trwb in complex with the non-hydrolisable ATP-analogue adpnp.
Analyse Plasmid coupling protein trwb in complex with the non-hydrolisable ATP-analogue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GL7
- Type
- protein
- Length
- 2,484 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conjugal transfer protein trwb
- UniProt
- Q04230
- Ligands
- ANP, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conjugal transfer protein trwb | protein | 411 | 45% helix, 17% strand | Q04230 |
| B | Conjugal transfer protein trwb | protein | 417 | 45% helix, 17% strand | Q04230 |
| D | Conjugal transfer protein trwb | protein | 417 | 45% helix, 18% strand | Q04230 |
| E | Conjugal transfer protein trwb | protein | 414 | 46% helix, 17% strand | Q04230 |
| F | Conjugal transfer protein trwb | protein | 413 | 46% helix, 17% strand | Q04230 |
| G | Conjugal transfer protein trwb | protein | 412 | 45% helix, 17% strand | Q04230 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains A, B, D, E, F, G
- CL · Chloride ion · ion · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.87 | 0.88 | 111 | empty |
| 2 | 1057 | 0.86 | 0.87 | 106 | empty |
| 3 | 1083 | 0.86 | 0.87 | 107 | empty |
| 4 | 1112 | 0.86 | 0.87 | 111 | empty |
| 5 | 1145 | 0.86 | 0.87 | 109 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2352 Ų buried · 24 hydrogen bonds · protein-protein
- A–G · 2316 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2306 Ų buried · 30 hydrogen bonds · protein-protein
- F–G · 2296 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2281 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1GL7 · Plasmid coupling protein TrwB in complex with the non-hydrolisable ATP-analogue ADPNP. · 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 Q04230
- Elsewhere: RCSB PDB 1GL7 · PDBe 1GL7 · UniProt Q04230
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