MolNFT v1 · #21107 · protein + DNA
Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule
1RZT · 5'-D(*CP*GP*GP*CP*AP*AP*CP*GP*CP*AP*C)-3': “Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule”. X-ray diffraction, 1 ligand (NA), 10 pockets (best druggability 0.77). MolNFT v1 #21107 on…
- PDB
- 1RZT
- Type
- protein + DNA
- Length
- 1,386 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*GP*CP*AP*AP*CP*GP*CP*AP*C)-3'; 5'-D(*GP*TP*GP*CP*G)-3'…
- EC
- 2.7.7.7
- UniProt
- Q9UGP5
- Ligands
- NA
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, F, J, N | 5'-D(*CP*GP*GP*CP*AP*AP*CP*GP*CP*AP*C)-3' | dna | 11 | — | — |
| C, G, K, O | 5'-D(*GP*TP*GP*CP*G)-3' | dna | 5 | — | — |
| 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, 16% strand | Q9UGP5 |
| E, I | DNA polymerase lambda (EC 2.7.7.7) | protein | 326 | 48% helix, 15% strand | Q9UGP5 |
Ligands and binding sites
- NA · Sodium ion · metal · 10 copies · chains B, D, F, H, J, L, C, A, G, E, K, I, O, M, P
- EDO · 1,2-ethanediol · additive · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.77 | 0.80 | 104 | empty |
| 2 | 850 | 0.74 | 0.79 | 71 | empty |
| 3 | 822 | 0.74 | 0.79 | 69 | empty |
| 4 | 833 | 0.74 | 0.79 | 77 | empty |
| 5 | 1178 | 0.72 | 0.76 | 75 | empty |
Interfaces
33 interfaces between chains.
- F–E · 600 Ų buried · 8 hydrogen bonds · protein-nucleic
- J–I · 596 Ų buried · 13 hydrogen bonds · protein-nucleic
- N–M · 583 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–A · 576 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–M · 524 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1RZT · Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA… · 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 1RZT · PDBe 1RZT · UniProt Q9UGP5
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