Research workbench
Arabidopsis thaliana NAA50 in complex with bisubstrate analogue CoA- ac-mvnal
Analyse Arabidopsis thaliana NAA50 in complex with bisubstrate analogue CoA- ac-mvnal in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z00
- Type
- protein
- Length
- 317 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA N-acyltransferases (nat) superfamily protein; Met-val-asn-ala-leu
- UniProt
- Q9LFM3
- Ligands
- CMC
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA N-acyltransferases (nat) superfamily protein | protein | 156 | 35% helix, 32% strand | Q9LFM3 |
| B | Acyl-CoA N-acyltransferases (nat) superfamily protein | protein | 151 | 35% helix, 35% strand | Q9LFM3 |
| C, D | Met-val-asn-ala-leu | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- CMC · Carboxymethyl coenzyme *A · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.70 | 0.79 | 56 | CMC |
| 2 | 215 | 0.58 | 0.79 | 26 | CMC |
| 3 | 68 | 0.37 | 0.78 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 571 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 469 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 447 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6Z00 · Arabidopsis thaliana Naa50 in complex with bisubstrate analogue CoA-Ac-MVNAL · 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 Q9LFM3
- Elsewhere: RCSB PDB 6Z00 · PDBe 6Z00 · UniProt Q9LFM3
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