Research workbench
Crystal structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap
Analyse Crystal structure of human DNA polymerase lambda in complex with a one… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XSL
- Type
- protein + DNA
- Length
- 1,389 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'; 5'-D(*GP*TP*GP*CP*GP*C)-3'…
- EC
- 2.7.7.7
- UniProt
- Q9UGP5
- Ligands
- NA, MG
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, F, J, N | 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3' | dna | 11 | — | — |
| C, G, K, O | 5'-D(*GP*TP*GP*CP*GP*C)-3' | dna | 6 | — | — |
| D, H, L, P | 5'-D(P*GP*CP*CP*G)-3' | dna | 4 | — | — |
| A, M | DNA polymerase lambda (EC 2.7.7.7) | protein | 327 | 48% helix, 15% strand | Q9UGP5 |
| E | DNA polymerase lambda (EC 2.7.7.7) | protein | 325 | 48% helix, 15% strand | Q9UGP5 |
| I | DNA polymerase lambda (EC 2.7.7.7) | protein | 326 | 48% helix, 16% strand | Q9UGP5 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains J, N, P, C, A, G, E, K, I, O, M
- MG · Magnesium ion · metal · 3 copies · chains B, D, F, H, L
- CAC · Cacodylate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.73 | 0.80 | 64 | empty |
| 2 | 608 | 0.72 | 0.80 | 56 | empty |
| 3 | 1090 | 0.71 | 0.75 | 59 | empty |
| 4 | 1011 | 0.70 | 0.75 | 55 | empty |
| 5 | 1100 | 0.70 | 0.75 | 56 | NA |
Interfaces
35 interfaces between chains.
- J–I · 616 Ų buried · 12 hydrogen bonds · protein-nucleic
- F–E · 608 Ų buried · 13 hydrogen bonds · protein-nucleic
- N–M · 607 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–A · 602 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–M · 534 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1XSL · Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap · the same entry in another collection · chain M against M, 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 Q9UGP5
- Elsewhere: RCSB PDB 1XSL · PDBe 1XSL · UniProt Q9UGP5
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