MolNFT v1 · #103681 · protein
E. COLI sliding clamp in complex with (R)-6-bromo-9-(2-((S)-1-carboxy- 2-phenylethylamino)-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2- carboxylic acid
4PNW · DNA polymerase III subunit beta: “E. COLI sliding clamp in complex with (R)-6-bromo-9-(2-((S)-1-carboxy…”. X-ray diffraction, 3 ligands (2VM, CA, CL), 6 pockets (best druggability 0.41). MolNFT v1 #103681 on GenesisL1: 3D structure…
- PDB
- 4PNW
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta
- EC
- 2.7.7.7
- UniProt
- U6NCW5
- Ligands
- 2VM, CA, CL
- Pockets
- 6 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 364 | 23% helix, 45% strand | U6NCW5 |
Ligands and binding sites
- 2VM · (2R)-6-bromo-9-(2-{[(1S)-1-carboxy-2-phenylethyl]amino}-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.41 | 0.75 | 22 | CA |
| 2 | 97 | 0.36 | 0.74 | 20 | CA |
| 3 | 53 | 0.31 | 0.76 | 14 | empty |
| 4 | 78 | 0.31 | 0.74 | 22 | empty |
| 5 | 61 | 0.31 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1298 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4PNW · E. coli sliding clamp in complex with (R)-6-bromo-9-(2-((S)-1-carboxy-2-phenylethylamino)… · the same entry in another collection · chain B against B, 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 U6NCW5
- Elsewhere: RCSB PDB 4PNW · PDBe 4PNW · UniProt U6NCW5
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