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Crystal structure of DNA polymerase sliding clamp from pseudomonas aeruginosa with ligand
Analyse Crystal structure of DNA polymerase sliding clamp from pseudomonas aeruginosa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TSZ
- Type
- protein
- Length
- 5,906 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta; ACE-gln-alc-asp-leu-zcl peptide
- EC
- 2.7.7.7
- UniProt
- V4MZL6
- Ligands
- ACE
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, K, L, M, O, P | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 363 | 21% helix, 44% strand | V4MZL6 |
| Q, R, S, T, U, V, X, Y, Z, 0, 1, 2, 3, 4, 5, 6 | ACE-gln-alc-asp-leu-zcl peptide | protein | 5 | 0% helix, 0% strand | — |
| F, G, H, I, J, N | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 366 | 21% helix, 43% strand | V4MZL6 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 16 copies · chains A, Q, B, R, C, S, D, T, E, U, F, V, G, X, H, Y, I, Z, J, 0, K, 1, L, 2, M, 3, N, 4, O, 5, P, 6
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.66 | 0.77 | 52 | empty |
| 2 | 626 | 0.66 | 0.76 | 52 | empty |
| 3 | 656 | 0.65 | 0.75 | 47 | empty |
| 4 | 657 | 0.65 | 0.75 | 40 | empty |
| 5 | 513 | 0.60 | 0.74 | 52 | empty |
Interfaces
40 interfaces between chains.
- G–H · 1313 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1310 Ų buried · 25 hydrogen bonds · protein-protein
- K–L · 1309 Ų buried · 25 hydrogen bonds · protein-protein
- I–J · 1306 Ų buried · 25 hydrogen bonds · protein-protein
- O–P · 1301 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 16 covalent (nonstandard, covalent ligand).
Compared structures
- 4TSZ · Crystal structure of DNA polymerase sliding clamp from Pseudomonas aeruginosa with ligand · the same entry in another collection · chain Q against Q, 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 V4MZL6
- Elsewhere: RCSB PDB 4TSZ · PDBe 4TSZ · UniProt V4MZL6
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