MolNFT v1 · #57337 · protein + DNA
Crystal structural analysis of hindiii restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 ångström resolution
3A4K · Type-2 restriction enzyme hindiii: “Crystal structural analysis of hindiii restriction endonuclease in complex with cognate DNA and divalent…”. X-ray diffraction, 2 ligands (MG, MN), 20 pockets (best druggability 0.79). MolNFT v1…
- 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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