MolNFT v1 · #153365 · protein

Crystal structure of aminotransferase crmg from actinoalloteichus sp. WH1-2216-6 in complex with amino donor L-ala

6JC7: “Crystal structure of aminotransferase crmg from actinoalloteichus sp. WH1-2216-6 in complex with amino donor…”. X-ray diffraction, 1 ligand (F0G), 14 pockets (best druggability 0.87). MolNFT v1 #153365 on GenesisL1: 3D structure…

PDB: 6JC7
Type: protein
Length: 2,044 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Crmg
UniProt: H8Y6N2
Ligands: F0G
Pockets: 14 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Crmg	protein	511	47% helix, 19% strand	H8Y6N2
C	Crmg	protein	510	46% helix, 19% strand	H8Y6N2
D	Crmg	protein	512	46% helix, 19% strand	H8Y6N2

Ligands and binding sites

F0G · (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 6 copies · chains A, B, C, D
ACY · Acetic acid · additive · 4 copies · chains B, C

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1032	0.87	0.88	140	F0G
2	785	0.84	0.87	89	F0G
3	612	0.84	0.89	75	F0G
4	615	0.84	0.88	78	F0G
5	77	0.56	0.87	22	empty

Interfaces

5 interfaces between chains.

A–B · 4724 Å² buried · 68 hydrogen bonds · protein-protein
C–D · 4724 Å² buried · 69 hydrogen bonds · protein-protein
A–C · 901 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 32 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 30 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6JC7 · Crystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in… · the same entry in another collection · chain D against D, 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 H8Y6N2
Elsewhere: RCSB PDB 6JC7 · PDBe 6JC7 · UniProt H8Y6N2

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