Research workbench
Structure of an accessory protein of the PCW3 relaxosome in complex with the origin of transfer (orit) DNA
Analyse Structure of an accessory protein of the PCW3 relaxosome in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VFX
- Type
- protein + DNA
- Length
- 983 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tcpk; Orit
- UniProt
- Q1PLI2
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, G | Tcpk | protein | 100 | 44% helix, 23% strand | Q1PLI2 |
| D | Tcpk | protein | 99 | 44% helix, 23% strand | Q1PLI2 |
| F | Tcpk | protein | 101 | 42% helix, 23% strand | Q1PLI2 |
| H | Tcpk | protein | 99 | 45% helix, 22% strand | Q1PLI2 |
| I, K, N, O | Orit | dna | 23 | — | — |
| J, L, M, P | Orit | dna | 23 | — | — |
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.69 | 0.78 | 56 | empty |
| 2 | 800 | 0.67 | 0.74 | 64 | empty |
| 3 | 559 | 0.62 | 0.75 | 55 | empty |
| 4 | 308 | 0.53 | 0.75 | 30 | empty |
| 5 | 188 | 0.50 | 0.77 | 29 | empty |
Interfaces
40 interfaces between chains.
- O–P · 1021 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- I–J · 1021 Ų buried · 102 hydrogen bonds · nucleic-nucleic
- M–N · 1018 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- K–L · 1013 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–B · 777 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5VFX · Structure of an accessory protein of the pCW3 relaxosome in complex with the origin of… · the same entry in another collection · chain P against P, 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 Q1PLI2
- Elsewhere: RCSB PDB 5VFX · PDBe 5VFX · UniProt Q1PLI2
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