Research workbench
Fitting of the C-terminal part of the short tail fibers into the cryo- EM reconstruction of T4 baseplate
Analyse Fitting of the C-terminal part of the short tail fibers into the cryo- EM… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PDI
- Type
- protein
- Length
- 5,004 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short tail fiber protein
- UniProt
- P10930
- Pockets
- 20 · best druggability 0.62
Structure
electron microscopy · 1 distinct chain · 0% 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 | Short tail fiber protein | protein | 278 | 0% helix, 0% strand | P10930 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.62 | 0.75 | 71 | empty |
| 2 | 379 | 0.62 | 0.75 | 72 | empty |
| 3 | 235 | 0.56 | 0.76 | 39 | empty |
| 4 | 241 | 0.55 | 0.76 | 38 | empty |
| 5 | 227 | 0.54 | 0.75 | 36 | empty |
Interfaces
18 interfaces between chains.
- A–B · 2123 Ų buried · 0 hydrogen bonds · protein-protein
- M–N · 2116 Ų buried · 0 hydrogen bonds · protein-protein
- G–H · 2115 Ų buried · 0 hydrogen bonds · protein-protein
- J–K · 2110 Ų buried · 0 hydrogen bonds · protein-protein
- P–Q · 2109 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1PDI · Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction… · 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 P10930
- Elsewhere: RCSB PDB 1PDI · PDBe 1PDI · UniProt P10930
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