MolNFT v1 · #39926 · protein
T4 polynucleotide KINASE/PHOSPHATASE with bound sulfate and magnesium.
2IA5: “T4 polynucleotide KINASE/PHOSPHATASE with bound sulfate and magnesium.”. X-ray diffraction, 3 ligands (ARS, MG, SO4), 20 pockets (best druggability 0.78). MolNFT v1 #39926 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2IA5
- Type
- protein
- Length
- 3,542 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polynucleotide kinase
- EC
- 2.7.1.78
- UniProt
- P06855
- Ligands
- ARS, MG, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 12 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polynucleotide kinase (EC 2.7.1.78) | protein | 297 | 44% helix, 19% strand | P06855 |
| B | Polynucleotide kinase (EC 2.7.1.78) | protein | 300 | 44% helix, 17% strand | P06855 |
| C | Polynucleotide kinase (EC 2.7.1.78) | protein | 299 | 43% helix, 17% strand | P06855 |
| D | Polynucleotide kinase (EC 2.7.1.78) | protein | 296 | 43% helix, 17% strand | P06855 |
| E | Polynucleotide kinase (EC 2.7.1.78) | protein | 293 | 42% helix, 19% strand | P06855 |
| F | Polynucleotide kinase (EC 2.7.1.78) | protein | 298 | 42% helix, 17% strand | P06855 |
| G | Polynucleotide kinase (EC 2.7.1.78) | protein | 294 | 46% helix, 16% strand | P06855 |
| H | Polynucleotide kinase (EC 2.7.1.78) | protein | 301 | 44% helix, 17% strand | P06855 |
| I | Polynucleotide kinase (EC 2.7.1.78) | protein | 289 | 44% helix, 17% strand | P06855 |
| J | Polynucleotide kinase (EC 2.7.1.78) | protein | 296 | 43% helix, 17% strand | P06855 |
| K | Polynucleotide kinase (EC 2.7.1.78) | protein | 288 | 45% helix, 17% strand | P06855 |
| L | Polynucleotide kinase (EC 2.7.1.78) | protein | 291 | 43% helix, 18% strand | P06855 |
Ligands and binding sites
- ARS · Arsenic · metal · 11 copies · chains A, B, C, D, E, F, G, H, I, J, K
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, H, J
- SO4 · Sulfate ion · ion · 36 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.78 | 0.80 | 93 | SO4 |
| 2 | 901 | 0.78 | 0.81 | 96 | SO4 |
| 3 | 910 | 0.77 | 0.80 | 90 | SO4 |
| 4 | 1007 | 0.77 | 0.79 | 93 | SO4 |
| 5 | 1005 | 0.77 | 0.79 | 88 | SO4 |
Interfaces
20 interfaces between chains.
- J–K · 1396 Ų buried · 19 hydrogen bonds · protein-protein
- E–H · 1394 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1393 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1377 Ų buried · 21 hydrogen bonds · protein-protein
- I–L · 1362 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2IA5 · T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium. · the same entry in another collection · chain A against A, 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 P06855
- Elsewhere: RCSB PDB 2IA5 · PDBe 2IA5 · UniProt P06855
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