MolNFT v1 · #83860 · protein + DNA
Time-resolved crystal structure of hindiii with 0SEC soaking
3WVG · Type-2 restriction enzyme hindiii: “Time-resolved crystal structure of hindiii with 0SEC soaking”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.79). MolNFT v1 #83860 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3WVG
- Type
- protein + DNA
- Length
- 1,288 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme hindiii; DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
- EC
- 3.1.21.4
- UniProt
- P43870
- Ligands
- NA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Type-2 restriction enzyme hindiii (EC 3.1.21.4) | protein | 298 | 60% helix, 11% strand | P43870 |
| G, H, K, L, E, F, I, J | DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, E, B, F, C, G, D, H
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.79 | 0.82 | 60 | empty |
| 2 | 907 | 0.78 | 0.81 | 62 | empty |
| 3 | 460 | 0.71 | 0.81 | 55 | empty |
| 4 | 189 | 0.71 | 0.88 | 32 | empty |
| 5 | 236 | 0.67 | 0.84 | 33 | empty |
Interfaces
28 interfaces between chains.
- A–B · 3481 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 3478 Ų buried · 31 hydrogen bonds · protein-protein
- C–H · 847 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–F · 842 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–E · 825 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 3WVG · Time-Resolved Crystal Structure of HindIII with 0sec soaking · the same entry in another collection · chain J against J, 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 P43870
- Elsewhere: RCSB PDB 3WVG · PDBe 3WVG · UniProt P43870
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