MolNFT v1 · #120616 · protein

Structure of transferase mutant-C23S,C199S

5H62: “Structure of transferase mutant-C23S,C199S”. X-ray diffraction, 2 ligands (UDP, MN), 5 pockets (best druggability 0.65). MolNFT v1 #120616 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H62
Type: protein
Length: 607 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transferase
Ligands: UDP, MN
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transferase	protein	306	42% helix, 21% strand	—
B	Transferase	protein	301	40% helix, 22% strand	—

Ligands and binding sites

UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	241	0.65	0.83	34	EDO, MN, UDP
2	403	0.62	0.77	40	MN, EDO, UDP
3	439	0.58	0.74	45	empty
4	59	0.39	0.79	15	empty
5	105	0.38	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 586 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5H62 · Structure of Transferase mutant-C23S,C199S · 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
Elsewhere: RCSB PDB 5H62 · PDBe 5H62

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