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X-ray structure of a KAPOSI'S sarcoma herpesvirus lana peptide bound to the nucleosomal core
Analyse X-ray structure of a KAPOSI'S sarcoma herpesvirus lana peptide bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZLA
- Type
- protein + DNA
- Length
- 1,064 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Palindromic 146BP human alpha-satellite DNA fragment; Histone H3; Histone H4; Xenopus…
- UniProt
- P62799
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, J | Palindromic 146BP human alpha-satellite DNA fragment | dna | 146 | — | — |
| A, E | Histone H3 | protein | 98 | 61% helix, 4% strand | — |
| B | Histone H4 | protein | 79 | 63% helix, 9% strand | P62799 |
| C | Xenopus laevis-like histone H2A | protein | 107 | 56% helix, 7% strand | — |
| D, H | Histone H2B | protein | 93 | 74% helix, 4% strand | — |
| F | Histone H4 | protein | 84 | 60% helix, 8% strand | P62799 |
| G | Xenopus laevis-like histone H2A | protein | 106 | 56% helix, 6% strand | — |
| K | Latent nuclear antigen | protein | 14 | 0% helix, 14% strand | — |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.76 | 0.86 | 52 | empty |
| 2 | 614 | 0.76 | 0.82 | 76 | empty |
| 3 | 343 | 0.74 | 0.86 | 47 | empty |
| 4 | 726 | 0.68 | 0.77 | 50 | empty |
| 5 | 553 | 0.67 | 0.77 | 49 | empty |
Interfaces
39 interfaces between chains.
- I–J · 6453 Ų buried · 582 hydrogen bonds · nucleic-nucleic
- C–D · 2633 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2615 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2576 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2550 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1ZLA · X-ray Structure of a Kaposi's sarcoma herpesvirus LANA peptide bound to the nucleosomal… · the same entry in another collection · chain I against I, 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 P62799
- Elsewhere: RCSB PDB 1ZLA · PDBe 1ZLA · UniProt P62799
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