MolNFT v1 · #61418 · protein
Crystal structure of the replication initiator protein encoded on plasmid PMV158 (repb), trigonal form, to 2.7 ang resolution
3DKX · Replication protein repb: “Crystal structure of the replication initiator protein encoded on plasmid PMV158 (repb), trigonal form, to…”. X-ray diffraction, 3 ligands (MN, MG, CL), 5 pockets (best druggability 0.73). MolNFT v1 #61418…
- PDB
- 3DKX
- Type
- protein
- Length
- 605 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication protein repb
- UniProt
- P13921
- Ligands
- MN, MG, CL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Replication protein repb | protein | 202 | 44% helix, 17% strand | P13921 |
| C | Replication protein repb | protein | 201 | 47% helix, 17% strand | P13921 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains 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 | 1051 | 0.73 | 0.77 | 81 | empty |
| 2 | 603 | 0.66 | 0.76 | 58 | empty |
| 3 | 240 | 0.58 | 0.78 | 24 | empty |
| 4 | 176 | 0.45 | 0.75 | 22 | empty |
| 5 | 78 | 0.35 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1480 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1359 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3DKX · Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (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 C against A, TM-score 0.87
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 3DKX · PDBe 3DKX · UniProt P13921
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