MolNFT v1 · #120617 · protein

Structure of transferase mutant-C23S,C199S

5H63: “Structure of transferase mutant-C23S,C199S”. X-ray diffraction, 2 ligands (UD1, MN), 10 pockets (best druggability 0.73). MolNFT v1 #120617 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H63
Type: protein
Length: 1,222 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transferase
Ligands: UD1, MN
Pockets: 10 · best druggability 0.73

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Transferase	protein	309	41% helix, 20% strand	—
C, D	Transferase	protein	302	40% helix, 22% strand	—

Ligands and binding sites

UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 4 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 6 copies · chains A, D, B, C

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	991	0.73	0.77	83	MN, UD1
2	704	0.71	0.78	65	empty
3	452	0.69	0.81	43	UD1, MN
4	278	0.67	0.83	33	UD1, MN
5	290	0.66	0.82	36	UD1, MN

Interfaces

3 interfaces between chains.

B–C · 620 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 610 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 508 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5H63 · 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 5H63 · PDBe 5H63

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