MolNFT v1 · #110225 · protein

Ensemble refinement of cystathione gamma lyase (CALE6) D7G from micromonospora echinospora

4XQ2: “Ensemble refinement of cystathione gamma lyase (CALE6) D7G from micromonospora echinospora”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.83). MolNFT v1 #110225 on GenesisL1: 3D structure, binding sites and…

PDB: 4XQ2
Type: protein
Length: 3,018 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CALE6
UniProt: Q8KNG3
Ligands: CL
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 37% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	CALE6	protein	376	36% helix, 16% strand	Q8KNG3
B, G, H	CALE6	protein	378	37% helix, 16% strand	Q8KNG3
C	CALE6	protein	379	37% helix, 17% strand	Q8KNG3
E	CALE6	protein	376	36% helix, 16% strand	Q8KNG3
F	CALE6	protein	377	39% helix, 15% strand	Q8KNG3

Ligands and binding sites

CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H
GOL · Glycerol · additive · 28 copies · chains A, C, B, D, E, F, G, H
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 8 copies · chains A, B, C, D, E, F, G, H
FMT · Formic acid · additive · 3 copies · chains C, F, G

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	1092	0.83	0.84	104	GOL
2	364	0.77	0.87	37	empty
3	83	0.77	0.97	19	empty
4	78	0.76	0.97	17	empty
5	336	0.76	0.87	36	empty

Interfaces

15 interfaces between chains.

C–D · 2174 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2107 Å² buried · 41 hydrogen bonds · protein-protein
G–H · 2093 Å² buried · 43 hydrogen bonds · protein-protein
E–F · 2044 Å² buried · 35 hydrogen bonds · protein-protein
A–D · 1631 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 modified (engineered, cofactor).

Compared structures

4XQ2 · Ensemble refinement of cystathione gamma lyase (CalE6) D7G from Micromonospora echinospora · 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 Q8KNG3
Elsewhere: RCSB PDB 4XQ2 · PDBe 4XQ2 · UniProt Q8KNG3

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