Research workbench
Crystal structure of the replication initiator protein encoded on plasmid PMV158 (repb), tetragonal form, to 3.6 ang resolution
Analyse Crystal structure of the replication initiator protein encoded on plasmid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DKY
- Type
- protein
- Length
- 1,161 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication protein repb
- UniProt
- P13921
- Ligands
- MN
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication protein repb | protein | 200 | 47% helix, 17% strand | P13921 |
| B, C | Replication protein repb | protein | 201 | 48% helix, 16% strand | P13921 |
| D | Replication protein repb | protein | 189 | 49% helix, 16% strand | P13921 |
| E | Replication protein repb | protein | 180 | 52% helix, 11% strand | P13921 |
| F | Replication protein repb | protein | 190 | 49% helix, 17% strand | P13921 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.73 | 0.77 | 80 | empty |
| 2 | 1001 | 0.72 | 0.76 | 90 | empty |
| 3 | 541 | 0.64 | 0.76 | 44 | empty |
| 4 | 364 | 0.54 | 0.74 | 30 | empty |
| 5 | 169 | 0.49 | 0.77 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1573 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1550 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1534 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1161 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 952 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3DKY · Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB)… · the same entry in another collection · chain F against F, 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 0.97
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 3DKY · PDBe 3DKY · UniProt P13921
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