MolNFT v1 · #120223 · protein + DNA
Crystal structure of complex between dmap-sh conjugated with a KAPOSI'S sarcoma herpesvirus lana peptide (5-15) and nucleosome core particle
5GTC · Histone H3.1: “Crystal structure of complex between dmap-sh conjugated with a KAPOSI'S sarcoma herpesvirus lana peptide…”. X-ray diffraction, 3 ligands (MN, CL, NH2), 20 pockets (best druggability 0.81). MolNFT v1 #120223 on…
- PDB
- 5GTC
- Type
- protein + DNA
- Length
- 1,062 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (146-mer)…
- UniProt
- P68431, P62805, P04908, P06899, D0UZU1
- Ligands
- MN, CL, NH2
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 10 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 97 | 64% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 78 | 63% helix, 8% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 108 | 55% helix, 6% strand | P04908 |
| D | Histone H2B type 1-J | protein | 93 | 74% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 98 | 66% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 86 | 58% helix, 8% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 107 | 55% helix, 6% strand | P04908 |
| H | Histone H2B type 1-J | protein | 92 | 75% helix, 4% strand | P06899 |
| I, J | DNA (146-mer) | dna | 146 | — | — |
| K | Lana peptide | protein | 11 | 0% helix, 18% strand | D0UZU1 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains E, F, I, J
- CL · Chloride ion · ion · 4 copies · chains A, C, D, J, E, G, H, I
- NH2 · Amino group · ion · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.81 | 0.84 | 81 | empty |
| 2 | 382 | 0.76 | 0.86 | 50 | empty |
| 3 | 367 | 0.75 | 0.86 | 39 | empty |
| 4 | 201 | 0.69 | 0.87 | 33 | empty |
| 5 | 331 | 0.67 | 0.82 | 40 | empty |
Interfaces
38 interfaces between chains.
- I–J · 6434 Ų buried · 665 hydrogen bonds · nucleic-nucleic
- C–D · 2647 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2629 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2612 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2513 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5GTC · Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma… · the same entry in another collection · chain A against A, 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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Every structure of UniProt D0UZU1
- Elsewhere: RCSB PDB 5GTC · PDBe 5GTC · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt D0UZU1
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