MolNFT v1 · #21411 · protein + DNA
Dpo with at matched
1S9F · 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3': “Dpo with at matched”. X-ray diffraction, 3 ligands (DDY, CA, MG), 14 pockets (best druggability 0.81). MolNFT v1 #21411 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1S9F
- Type
- protein + DNA
- Length
- 1,484 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DDY, CA, MG
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, G, H | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3' | dna | 13 | — | — |
| I, J, K, L | 5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)- 3' | dna | 17 | — | — |
| A, B, C, D | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 45% helix, 25% strand | Q97W02 |
Ligands and binding sites
- DDY · 2',3'-dideoxycytosine-5'-diphosphate · ligand · 4 copies · chains E, I, A, F, J, B, G, K, C, H, L, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains E, A, F, B, G, C, H, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.81 | 0.82 | 77 | CA, DDY |
| 2 | 1069 | 0.80 | 0.82 | 71 | CA, DDY |
| 3 | 1178 | 0.80 | 0.82 | 79 | CA, DDY |
| 4 | 939 | 0.79 | 0.81 | 66 | empty |
| 5 | 786 | 0.75 | 0.80 | 47 | empty |
Interfaces
19 interfaces between chains.
- K–C · 1115 Ų buried · 27 hydrogen bonds · protein-nucleic
- I–A · 1107 Ų buried · 22 hydrogen bonds · protein-nucleic
- J–B · 1086 Ų buried · 24 hydrogen bonds · protein-nucleic
- L–D · 1014 Ų buried · 21 hydrogen bonds · protein-nucleic
- F–B · 637 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 1S9F · DPO with AT matched · the same entry in another collection · chain D against D, 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 Q97W02
- Elsewhere: RCSB PDB 1S9F · PDBe 1S9F · UniProt Q97W02
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