Research workbench
Crystal structure of npudnae intein
Analyse Crystal structure of npudnae intein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KL5
- Type
- protein
- Length
- 282 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III, alpha subunit, nucleic acid binding, ob-fold, TRNA/HELICASE-type…
- EC
- 2.7.7.7
- UniProt
- B2J066, B2J821
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III, alpha subunit, nucleic acid binding, ob-fold, TRNA/HELICASE-type chimeric construct (EC 2.7.7.7) | protein | 140 | 11% helix, 54% strand | B2J066, B2J821 |
| B | DNA polymerase III, alpha subunit, nucleic acid binding, ob-fold, TRNA/HELICASE-type chimeric construct (EC 2.7.7.7) | protein | 142 | 13% helix, 52% strand | B2J066, B2J821 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.49 | 0.82 | 13 | empty |
| 2 | 90 | 0.48 | 0.81 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 581 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4KL5 · Crystal structure of NpuDnaE intein · 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 B2J066
- Every structure of UniProt B2J821
- Elsewhere: RCSB PDB 4KL5 · PDBe 4KL5 · UniProt B2J066 · UniProt B2J821
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