MolNFT v1 · #80738 · protein + DNA
Structure of T4 bacteriophage clamp loader bound to closed clamp, DNA and ATP analog and ADP
3U61 · DNA polymerase accessory protein 44: “Structure of T4 bacteriophage clamp loader bound to closed clamp, DNA and ATP analog and ADP”. X-ray diffraction, 3 ligands (08T, ADP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #80738…
- PDB
- 3U61
- Type
- protein + DNA
- Length
- 2,110 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase accessory protein 44; DNA polymerase accessory protein 62; DNA polymerase…
- UniProt
- P04526, P04527, P04525
- Ligands
- 08T, ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 9 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA polymerase accessory protein 44 | protein | 305 | 58% helix, 10% strand | P04526 |
| C | DNA polymerase accessory protein 44 | protein | 319 | 58% helix, 10% strand | P04526 |
| D | DNA polymerase accessory protein 44 | protein | 320 | 56% helix, 9% strand | P04526 |
| E | DNA polymerase accessory protein 44 | protein | 294 | 56% helix, 9% strand | P04526 |
| A | DNA polymerase accessory protein 62 | protein | 178 | 59% helix, 0% strand | P04527 |
| G, H | DNA polymerase processivity component | protein | 228 | 18% helix, 42% strand | P04525 |
| F | DNA polymerase processivity component | protein | 222 | 18% helix, 41% strand | P04525 |
| I | Template DNA strand | dna | 8 | — | — |
| J | Primer DNA strand | dna | 8 | — | — |
Ligands and binding sites
- 08T · [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium · ligand · 2 copies · chains C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · 3 copies · chains B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.85 | 0.87 | 87 | empty |
| 2 | 141 | 0.79 | 0.96 | 28 | 08T |
| 3 | 139 | 0.78 | 0.96 | 27 | 08T, MG |
| 4 | 206 | 0.77 | 0.91 | 35 | empty |
| 5 | 950 | 0.75 | 0.78 | 61 | empty |
Interfaces
28 interfaces between chains.
- C–D · 2152 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2048 Ų buried · 36 hydrogen bonds · protein-protein
- E–A · 1373 Ų buried · 22 hydrogen bonds · protein-protein
- B–A · 1369 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1304 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3U61 · Structure of T4 Bacteriophage Clamp Loader Bound To Closed Clamp, DNA and ATP Analog and… · the same entry in another collection · chain B against B, 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 P04526
- Every structure of UniProt P04527
- Every structure of UniProt P04525
- Elsewhere: RCSB PDB 3U61 · PDBe 3U61 · UniProt P04526 · UniProt P04527 · UniProt P04525
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