MolNFT v1 · #154671 · protein + DNA
Cryo-EM structure of human MLL3-ubncp complex (4.0 ångström)
6KIW · Histone H3: “Cryo-EM structure of human MLL3-ubncp complex (4.0 ångström)”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.82). MolNFT v1 #154671 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KIW
- Type
- protein + DNA
- Length
- 2,098 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B 1.1; DNA (144-mer); DNA (145-mer)…
- EC
- 2.1.1.43
- UniProt
- A0A310TTQ1, P62799, Q6AZJ8, P02281, Q8NEZ4, Q15291, P62979, P61964, Q9UBL3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 14 distinct chains · 26% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3 | protein | 97 | 66% helix, 4% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 82 | 60% helix, 9% strand | P62799 |
| C | Histone H2A | protein | 107 | 49% helix, 4% strand | Q6AZJ8 |
| D | Histone H2B 1.1 | protein | 92 | 74% helix, 2% strand | P02281 |
| F | Histone H4 | protein | 81 | 62% helix, 6% strand | P62799 |
| G | Histone H2A | protein | 104 | 55% helix, 6% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 94 | 73% helix, 3% strand | P02281 |
| I | DNA (144-mer) | dna | 144 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| K | Histone-lysine N-methyltransferase 2C (EC 2.1.1.43) | protein | 156 | 13% helix, 16% strand | Q8NEZ4 |
| N | Retinoblastoma-binding protein 5 | protein | 347 | 2% helix, 32% strand | Q15291 |
| O | Ubiquitin | protein | 76 | 14% helix, 12% strand | P62979 |
| R | Wd repeat-containing protein 5 | protein | 300 | 0% helix, 27% strand | P61964 |
| T | SET1/ASH2 histone methyltransferase complex subunit ASH2 | protein | 176 | 2% helix, 31% strand | Q9UBL3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 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 | 910 | 0.82 | 0.84 | 63 | empty |
| 2 | 1123 | 0.80 | 0.81 | 92 | empty |
| 3 | 469 | 0.77 | 0.85 | 62 | empty |
| 4 | 515 | 0.77 | 0.84 | 50 | empty |
| 5 | 600 | 0.75 | 0.82 | 47 | empty |
Interfaces
53 interfaces between chains.
- I–J · 6551 Ų buried · 525 hydrogen bonds · nucleic-nucleic
- E–F · 2612 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2607 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2587 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 2586 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6KIW · Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) · the same entry in another collection · chain T against T, 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 A0A310TTQ1
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt Q8NEZ4
- Every structure of UniProt Q15291
- Every structure of UniProt P62979
- Every structure of UniProt P61964
- Every structure of UniProt Q9UBL3
- Elsewhere: RCSB PDB 6KIW · PDBe 6KIW · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt Q8NEZ4 · UniProt Q15291 · UniProt P62979 · UniProt P61964 · UniProt Q9UBL3
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