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Open and closed ternary complex of R283K DNA polymerase beta with a dctp analog in the same asymmetric unit
Analyse Open and closed ternary complex of R283K DNA polymerase beta with a dctp analog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F5R
- Type
- protein + DNA
- Length
- 708 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(P*GP*TP*CP*GP*G)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- 6CF, NA, MN
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 325 | 50% helix, 13% strand | P06746 |
| B | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 321 | 51% helix, 13% strand | P06746 |
| D, C | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| P, G | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') | dna | 10 | — | — |
| T, F | DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3') | dna | 16 | — | — |
Ligands and binding sites
- 6CF · 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine · ligand · 2 copies · chains A, P, T, B, G, F
- NA · Sodium ion · metal · 4 copies · chains A, P, B, T, G
- MN · Manganese (II) ion · metal · 4 copies · chains B, G, D, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.75 | 0.79 | 86 | 6CF |
| 2 | 927 | 0.74 | 0.78 | 70 | MN, 6CF |
| 3 | 267 | 0.64 | 0.82 | 28 | empty |
| 4 | 248 | 0.60 | 0.80 | 26 | empty |
| 5 | 244 | 0.53 | 0.76 | 36 | empty |
Interfaces
12 interfaces between chains.
- B–F · 715 Ų buried · 15 hydrogen bonds · protein-nucleic
- G–F · 473 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- P–T · 471 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–T · 434 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 388 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4F5R · Open and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the… · the same entry in another collection · chain C against C, TM-score 1.00
- P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P06746
- Elsewhere: RCSB PDB 4F5R · PDBe 4F5R · UniProt P06746
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