Research workbench
Structure of the NAP1 H2A H2B complex
Analyse Structure of the NAP1 H2A H2B complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G2E
- Type
- protein
- Length
- 4,056 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleosome assembly protein; Histone H2A type 1; Histone H2B 1.1
- UniProt
- P25293, P06897, P02281
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M, Q, U | Nucleosome assembly protein | protein | 252 | 46% helix, 13% strand | P25293 |
| B, F, J, N, R, V | Nucleosome assembly protein | protein | 245 | 49% helix, 13% strand | P25293 |
| C, G, K, O, S, W | Histone H2A type 1 | protein | 90 | 62% helix, 4% strand | P06897 |
| D, H, L, P, T, X | Histone H2B 1.1 | protein | 89 | 79% helix, 4% strand | P02281 |
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 | 978 | 0.76 | 0.78 | 94 | empty |
| 2 | 954 | 0.74 | 0.77 | 100 | empty |
| 3 | 507 | 0.73 | 0.82 | 54 | empty |
| 4 | 645 | 0.71 | 0.78 | 53 | empty |
| 5 | 580 | 0.71 | 0.79 | 51 | empty |
Interfaces
53 interfaces between chains.
- M–N · 3492 Ų buried · 36 hydrogen bonds · protein-protein
- U–V · 3478 Ų buried · 36 hydrogen bonds · protein-protein
- Q–R · 3476 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 3459 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3424 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5G2E · Structure of the Nap1 H2A H2B complex · the same entry in another collection · chain K against K, 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 P25293
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 5G2E · PDBe 5G2E · UniProt P25293 · UniProt P06897 · UniProt P02281
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