MolNFT v1 · #156605 · protein
Crystal structure of lambda exonuclease in complex with the red beta C-terminal domain
6M9K: “Crystal structure of lambda exonuclease in complex with the red beta C-terminal domain”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.75). MolNFT v1 #156605 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6M9K
- Type
- protein
- Length
- 873 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exonuclease; Recombination protein bet
- EC
- 3.1.11.3
- UniProt
- P03697, P03698
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Exonuclease (EC 3.1.11.3) | protein | 226 | 49% helix, 14% strand | P03697 |
| B | Exonuclease (EC 3.1.11.3) | protein | 225 | 47% helix, 13% strand | P03697 |
| D | Recombination protein bet | protein | 67 | 70% helix, 3% strand | P03698 |
| E | Recombination protein bet | protein | 66 | 71% helix, 3% strand | P03698 |
| F | Recombination protein bet | protein | 63 | 73% helix, 3% strand | P03698 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.75 | 0.80 | 61 | SO4 |
| 2 | 802 | 0.74 | 0.79 | 69 | SO4 |
| 3 | 773 | 0.73 | 0.78 | 65 | SO4 |
| 4 | 183 | 0.45 | 0.74 | 21 | empty |
| 5 | 139 | 0.41 | 0.74 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–D · 756 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 752 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 732 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 683 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 668 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6M9K · Crystal structure of lambda exonuclease in complex with the Red beta C-terminal domain · the same entry in another collection · chain A against A, 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 P03697
- Every structure of UniProt P03698
- Elsewhere: RCSB PDB 6M9K · PDBe 6M9K · UniProt P03697 · UniProt P03698
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