Research workbench
Crystal structure of the ba-soaked C2 crystal form of PMV158 replication initiator repb (P3221 space group)
Analyse Crystal structure of the ba-soaked C2 crystal form of PMV158 replication… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U87
- Type
- protein
- Length
- 593 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication protein repb
- UniProt
- P13921
- Ligands
- BA, MN, CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication protein repb | protein | 191 | 50% helix, 16% strand | P13921 |
| B, C | Replication protein repb | protein | 201 | 48% helix, 16% strand | P13921 |
Ligands and binding sites
- BA · Barium ion · metal · 9 copies · chains B, C
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.72 | 0.76 | 74 | BA |
| 2 | 317 | 0.58 | 0.77 | 28 | empty |
| 3 | 200 | 0.50 | 0.76 | 28 | MN |
| 4 | 213 | 0.47 | 0.74 | 26 | BA |
| 5 | 150 | 0.41 | 0.74 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1465 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1365 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4U87 · Crystal structure of the Ba-soaked C2 crystal form of pMV158 replication initiator RepB… · the same entry in another collection · chain A against A, TM-score 1.00
- P13921 · AlphaFold monomer V2.0 prediction for replication protein repb (P13921) · a predicted model of the same protein · chain B against A, TM-score 0.83
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 P13921
- Elsewhere: RCSB PDB 4U87 · PDBe 4U87 · UniProt P13921
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