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Crystal Structure Analysis of Ard1 from Thermoplasma volcanium

Analyse Crystal Structure Analysis of Ard1 from Thermoplasma volcanium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PV6
Type: protein
Length: 2,402 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.32
Source: Thermoplasma volcanium
Molecule: N-terminal acetyltransferase complex subunit [ARD1]
UniProt: Q97CT7
Ligands: ACO, COA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · resolution 3.32 · 10 distinct chains · 34% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, H	N-terminal acetyltransferase complex subunit [ARD1]	protein	153	34% helix, 31% strand	Q97CT7
D, P	N-terminal acetyltransferase complex subunit [ARD1]	protein	147	34% helix, 32% strand	Q97CT7
G, A	N-terminal acetyltransferase complex subunit [ARD1]	protein	154	35% helix, 32% strand	Q97CT7
I	N-terminal acetyltransferase complex subunit [ARD1]	protein	151	34% helix, 34% strand	Q97CT7
K, O	N-terminal acetyltransferase complex subunit [ARD1]	protein	149	32% helix, 32% strand	Q97CT7
M, N, B	N-terminal acetyltransferase complex subunit [ARD1]	protein	148	34% helix, 32% strand	Q97CT7
F	N-terminal acetyltransferase complex subunit [ARD1]	protein	150	34% helix, 31% strand	Q97CT7
J	N-terminal acetyltransferase complex subunit [ARD1]	protein	151	36% helix, 32% strand	Q97CT7
L	N-terminal acetyltransferase complex subunit [ARD1]	protein	149	38% helix, 32% strand	Q97CT7
E	N-terminal acetyltransferase complex subunit [ARD1]	protein	151	34% helix, 32% strand	Q97CT7

Ligands and binding sites

ACO · Acetyl coenzyme *A · ligand · 7 copies · chains C, G, I, F, H, J, E
COA · Coenzyme A · ligand · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1071	0.86	0.87	127	ACO
2	534	0.85	0.91	90	empty
3	526	0.83	0.89	76	ACO
4	509	0.83	0.90	70	empty
5	1002	0.82	0.83	99	empty

Interfaces

33 interfaces between chains.

A–B · 708 Å² buried · 9 hydrogen bonds · protein-protein
G–K · 694 Å² buried · 6 hydrogen bonds · protein-protein
I–M · 671 Å² buried · 5 hydrogen bonds · protein-protein
K–E · 628 Å² buried · 8 hydrogen bonds · protein-protein
H–L · 621 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4PV6 · Crystal structure analysis of ARD1 from thermoplasma volcanium · 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 Q97CT7
Elsewhere: RCSB PDB 4PV6 · PDBe 4PV6 · UniProt Q97CT7

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