MolNFT v1 · #116900 · protein

Crystal structure of tet aminopeptidase from marine sediment archaeon thaumarchaeota archaeon scgc ab-539-E09

5DS0 · Peptidase M42: “Crystal structure of tet aminopeptidase from marine sediment archaeon thaumarchaeota archaeon scgc ab-539-E09”. X-ray diffraction, 1 ligand (CO), 20 pockets (best druggability 0.80). MolNFT v1 #116900 on GenesisL1…

PDB: 5DS0
Type: protein
Length: 4,276 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidase M42
UniProt: M7T295
Ligands: CO
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 7 distinct chains · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Peptidase M42	protein	357	32% helix, 27% strand	M7T295
B	Peptidase M42	protein	356	32% helix, 28% strand	M7T295
C	Peptidase M42	protein	359	32% helix, 28% strand	M7T295
D	Peptidase M42	protein	358	32% helix, 28% strand	M7T295
F, G, H, J, K	Peptidase M42	protein	356	31% helix, 28% strand	M7T295
I	Peptidase M42	protein	354	32% helix, 28% strand	M7T295
L	Peptidase M42	protein	355	31% helix, 28% strand	M7T295

Ligands and binding sites

CO · Cobalt (II) ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
GOL · Glycerol · additive · 15 copies · chains A, B, D, C, L, E, F, G, H, I, J, K

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	1066	0.80	0.81	103	empty
2	445	0.75	0.84	25	empty
3	420	0.74	0.84	33	empty
4	444	0.74	0.84	28	empty
5	491	0.74	0.82	61	empty

Interfaces

30 interfaces between chains.

C–L · 2531 Å² buried · 31 hydrogen bonds · protein-protein
B–D · 2500 Å² buried · 30 hydrogen bonds · protein-protein
J–K · 2469 Å² buried · 31 hydrogen bonds · protein-protein
H–I · 2460 Å² buried · 31 hydrogen bonds · protein-protein
E–F · 2441 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 168 modified (engineered).

Compared structures

5DS0 · Crystal structure of TET aminopeptidase from marine sediment archaeon Thaumarchaeota… · 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 M7T295
Elsewhere: RCSB PDB 5DS0 · PDBe 5DS0 · UniProt M7T295

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