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Crystal structure of a pentameric capsid protein isolated from metagenomic phage sequences (casp)
Analyse Crystal structure of a pentameric capsid protein isolated from metagenomic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DMI
- Type
- protein
- Length
- 838 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- Ligands
- NA
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 168 | 11% helix, 48% strand | — |
| B | Capsid protein | protein | 169 | 11% helix, 49% strand | — |
| C | Capsid protein | protein | 167 | 11% helix, 50% strand | — |
| D | Capsid protein | protein | 169 | 11% helix, 47% strand | — |
| E | Capsid protein | protein | 165 | 11% helix, 49% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, C, B, E, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.83 | 0.84 | 152 | empty |
| 2 | 996 | 0.70 | 0.75 | 104 | empty |
Interfaces
10 interfaces between chains.
- B–D · 2428 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2422 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 2387 Ų buried · 38 hydrogen bonds · protein-protein
- B–E · 2296 Ų buried · 37 hydrogen bonds · protein-protein
- A–E · 2211 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 4DMI · Crystal Structure of a Pentameric Capsid Protein Isolated from Metagenomic Phage… · 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
- Elsewhere: RCSB PDB 4DMI · PDBe 4DMI
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