MolNFT v1 · #66142 · protein
Crystal structure of apo DUT1P from saccharomyces cerevisiae
3HHQ · Deoxyuridine 5'-triphosphate nucleotidohydrolase: “Crystal structure of apo DUT1P from saccharomyces cerevisiae”. X-ray diffraction, 3 ligands (NA, SO4, CL), 20 pockets (best druggability 0.81). MolNFT v1 #66142 on GenesisL1: 3D…
- PDB
- 3HHQ
- Type
- protein
- Length
- 3,045 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine 5'-triphosphate nucleotidohydrolase
- EC
- 3.6.1.23
- UniProt
- P33317
- Ligands
- NA, SO4, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 11 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 126 | 6% helix, 47% strand | P33317 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 128 | 5% helix, 45% strand | P33317 |
| C, E, T | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 128 | 5% helix, 46% strand | P33317 |
| D, N, P, Q | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 125 | 6% helix, 46% strand | P33317 |
| F, H, J, X | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 126 | 6% helix, 45% strand | P33317 |
| G, O, R, U, V | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 127 | 6% helix, 46% strand | P33317 |
| I | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 127 | 6% helix, 47% strand | P33317 |
| K | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 127 | 6% helix, 45% strand | P33317 |
| L, S | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 127 | 6% helix, 46% strand | P33317 |
| M | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 130 | 5% helix, 44% strand | P33317 |
| W | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 130 | 5% helix, 44% strand | P33317 |
Ligands and binding sites
- NA · Sodium ion · metal · 14 copies · chains A, B, C, E, F, K, L, M, N, O, P, Q, S, U, T, V
- SO4 · Sulfate ion · ion · 35 copies · chains A, B, C, D, E, F, G, K, H, I, X, J, L, M, N, O, Q, P, R, S, T, U, V, W
- CL · Chloride ion · ion · 17 copies · chains B, C, D, E, F, I, J, L, N, Q, R, T, U, V
- EDO · 1,2-ethanediol · additive · 34 copies · chains D, F, E, K, G, J, L, M, N, O, P, Q, R, S, T, U, V, X, W
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains H, K, J, L, D, M, N, O, W, X, F
- GOL · Glycerol · additive · chains T, U
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 | 944 | 0.81 | 0.83 | 75 | SO4 |
| 2 | 798 | 0.80 | 0.83 | 68 | SO4 |
| 3 | 120 | 0.79 | 0.98 | 26 | EDO |
| 4 | 112 | 0.78 | 0.98 | 27 | empty |
| 5 | 114 | 0.78 | 0.98 | 30 | EDO |
Interfaces
64 interfaces between chains.
- A–B · 1537 Ų buried · 22 hydrogen bonds · protein-protein
- J–K · 1511 Ų buried · 21 hydrogen bonds · protein-protein
- S–T · 1510 Ų buried · 16 hydrogen bonds · protein-protein
- M–N · 1494 Ų buried · 18 hydrogen bonds · protein-protein
- W–X · 1487 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3HHQ · Crystal structure of apo dUT1p from Saccharomyces cerevisiae · the same entry in another collection · chain K against K, 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 P33317
- Elsewhere: RCSB PDB 3HHQ · PDBe 3HHQ · UniProt P33317
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