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Crystal structure of N-terminus deletion mutant of mycobacterium avium diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase

Analyse Crystal structure of N-terminus deletion mutant of mycobacterium avium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AF2
Type: protein
Length: 566 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hit domain-containing protein
UniProt: A0A2A2ZGT3
Ligands: SPM
Pockets: 14 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hit domain-containing protein	protein	143	33% helix, 20% strand	A0A2A2ZGT3
B	Hit domain-containing protein	protein	141	33% helix, 20% strand	A0A2A2ZGT3
C	Hit domain-containing protein	protein	138	39% helix, 20% strand	A0A2A2ZGT3
D	Hit domain-containing protein	protein	144	35% helix, 19% strand	A0A2A2ZGT3

Ligands and binding sites

SPM · Spermine · ligand · 3 copies · chains A, B, D
1PE · Pentaethylene glycol · additive · 2 copies · chains A, D
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	70	0.76	0.99	16	empty
2	55	0.74	0.99	16	empty
3	180	0.54	0.79	32	empty
4	342	0.53	0.74	26	empty
5	321	0.51	0.73	24	empty

Interfaces

5 interfaces between chains.

B–D · 1134 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 1101 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 274 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 200 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 193 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6AF2 · Crystal structure of N-terminus deletion mutant of Mycobacterium avium diadenosine… · 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 A0A2A2ZGT3
Elsewhere: RCSB PDB 6AF2 · PDBe 6AF2 · UniProt A0A2A2ZGT3

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