MolNFT v2 · #219887 · protein + DNA
Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome
8SIY · Leucine-rich repeat and WD repeat-containing protein 1: “Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome”. Electron microscopy at 2.9, 20 pockets (best druggability 0.77). MolNFT v2 #219887 on…
- PDB
- 8SIY
- Type
- protein + DNA
- Length
- 1,412 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Rattus norvegicus; synthetic construct; Xenopus laevis
- Molecule
- Leucine-rich repeat and WD repeat-containing protein 1; Histone H3.2; Histone H4; Histone…
- UniProt
- A0A140UHX1, P84233, A0A8J1LTD2, P06897, P02281, Q75PQ8
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · resolution 2.9 · 11 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich repeat and WD repeat-containing protein 1 | protein | 341 | 4% helix, 48% strand | A0A140UHX1 |
| C, G | Histone H3.2 | protein | 96 | 67% helix, 4% strand | P84233 |
| D | Histone H4 | protein | 79 | 63% helix, 9% strand | A0A8J1LTD2 |
| E | Histone H2A | protein | 108 | 54% helix, 6% strand | P06897 |
| F | Histone H2B | protein | 94 | 74% helix, 4% strand | P02281 |
| H | Histone H4 | protein | 86 | 57% helix, 8% strand | A0A8J1LTD2 |
| I | Histone H2A | protein | 107 | 54% helix, 7% strand | P06897 |
| J | Histone H2B | protein | 93 | 75% helix, 4% strand | P02281 |
| K | Widom 601 DNA | dna | 147 | — | — |
| L | Widom 601 DNA | dna | 147 | — | — |
| B | Origin recognition complex subunit 2 | protein | 18 | 17% helix, 28% strand | Q75PQ8 |
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 | 602 | 0.77 | 0.83 | 65 | empty |
| 2 | 447 | 0.75 | 0.84 | 53 | empty |
| 3 | 448 | 0.74 | 0.84 | 43 | empty |
| 4 | 789 | 0.72 | 0.78 | 64 | empty |
| 5 | 593 | 0.71 | 0.79 | 48 | empty |
Interfaces
41 interfaces between chains.
- K–L · 6591 Ų buried · 488 hydrogen bonds · nucleic-nucleic
- G–H · 2642 Ų buried · 26 hydrogen bonds · protein-protein
- I–J · 2598 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2567 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2492 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
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 A0A140UHX1
- Every structure of UniProt P84233
- Every structure of UniProt A0A8J1LTD2
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Every structure of UniProt Q75PQ8
- Elsewhere: RCSB PDB 8SIY · PDBe 8SIY · UniProt A0A140UHX1 · UniProt P84233 · UniProt A0A8J1LTD2 · UniProt P06897 · UniProt P02281 · UniProt Q75PQ8
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