Research workbench
Cryo-EM structure of human natb complex
Analyse Cryo-EM structure of human natb complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VP9
- Type
- protein
- Length
- 1,077 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-alpha-acetyltransferase 20; N-alpha-acetyltransferase 25, natb auxiliary subunit; Mdvfm…
- EC
- 2.3.1.254
- UniProt
- P61599, Q14CX7
- Ligands
- CMC
- Pockets
- 14 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 56% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-alpha-acetyltransferase 20 (EC 2.3.1.254) | protein | 158 | 22% helix, 19% strand | P61599 |
| B | N-alpha-acetyltransferase 25, natb auxiliary subunit | protein | 914 | 63% helix, 0% strand | Q14CX7 |
| C | Mdvfm peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- CMC · Carboxymethyl coenzyme *A · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.81 | 0.83 | 86 | CMC |
| 2 | 460 | 0.65 | 0.77 | 44 | empty |
| 3 | 245 | 0.60 | 0.80 | 36 | empty |
| 4 | 371 | 0.59 | 0.76 | 35 | empty |
| 5 | 124 | 0.54 | 0.82 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2413 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 497 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6VP9 · Cryo-EM structure of human NatB complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q14CX7 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 25, natb auxiliary… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P61599 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 20 (P61599) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P61599
- Every structure of UniProt Q14CX7
- Elsewhere: RCSB PDB 6VP9 · PDBe 6VP9 · UniProt P61599 · UniProt Q14CX7
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