Research workbench
Cryo-EM structure of conjugative pili from carbapenem-resistant klebsiella pneumoniae
Analyse Cryo-EM structure of conjugative pili from carbapenem-resistant klebsiella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JSV
- Type
- protein
- Length
- 2,706 residues
- Chains
- 41
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pilin
- UniProt
- A0A2U0MUX0
- Ligands
- LHG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o | Pilin | protein | 66 | 79% helix, 0% strand | A0A2U0MUX0 |
Ligands and binding sites
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 41 copies · chains A, B, I, J, S, D, G, L, Q, C, H, K, U, E, F, N, O, M, W, P, Y, R, a, T, c, V, e, X, g, Z, i, b, k, d, m, f, o, h, j, l, n
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.84 | 0.88 | 38 | LHG |
| 2 | 609 | 0.83 | 0.87 | 39 | LHG |
| 3 | 575 | 0.83 | 0.88 | 37 | LHG |
| 4 | 593 | 0.83 | 0.87 | 37 | LHG |
| 5 | 596 | 0.83 | 0.87 | 36 | LHG |
Interfaces
132 interfaces between chains.
- B–I · 1046 Ų buried · 10 hydrogen bonds · protein-protein
- Q–a · 1046 Ų buried · 10 hydrogen bonds · protein-protein
- P–Z · 1045 Ų buried · 10 hydrogen bonds · protein-protein
- D–N · 1044 Ų buried · 10 hydrogen bonds · protein-protein
- E–O · 1044 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7JSV · Cryo-EM structure of conjugative pili from carbapenem-resistant Klebsiella pneumoniae · the same entry in another collection · chain U against U, 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 A0A2U0MUX0
- Elsewhere: RCSB PDB 7JSV · PDBe 7JSV · UniProt A0A2U0MUX0
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