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Crystal structural analysis of hindiii restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 ångström resolution
Analyse Crystal structural analysis of hindiii restriction endonuclease in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A4K
- Type
- protein + DNA
- Length
- 1,261 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme hindiii; DNA (5'-D(*GP*CP*CP*A)-3'); DNA…
- EC
- 3.1.21.4
- UniProt
- P43870
- Ligands
- MG, MN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Type-2 restriction enzyme hindiii (EC 3.1.21.4) | protein | 297 | 59% helix, 12% strand | P43870 |
| D | Type-2 restriction enzyme hindiii (EC 3.1.21.4) | protein | 298 | 58% helix, 11% strand | P43870 |
| E, G, I, K | DNA (5'-D(*GP*CP*CP*A)-3') | dna | 4 | — | — |
| F, H, J, L | DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3') | dna | 8 | — | — |
| M, N | DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, E, F, C, G, H, B, I, J, D, K, L
- MN · Manganese (II) ion · metal · 4 copies · chains A, F, C, H, B, J, D, L
- ACT · Acetate ion · additive · 4 copies · chains C, B, D
- GOL · Glycerol · additive · 2 copies · chains A, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.79 | 0.83 | 60 | empty |
| 2 | 862 | 0.79 | 0.82 | 60 | empty |
| 3 | 112 | 0.76 | 0.97 | 15 | empty |
| 4 | 117 | 0.76 | 0.96 | 18 | empty |
| 5 | 125 | 0.74 | 0.94 | 18 | empty |
Interfaces
33 interfaces between chains.
- C–D · 3474 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 3466 Ų buried · 32 hydrogen bonds · protein-protein
- C–B · 666 Ų buried · 11 hydrogen bonds · protein-protein
- D–L · 622 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 619 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3A4K · Crystal structural analysis of HindIII restriction endonuclease in complex with cognate… · the same entry in another collection · chain N against N, 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 3A4K · PDBe 3A4K · UniProt P43870
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