MolNFT v1 · #21256 · protein

Yhch protein (HI0227) copper complex

1S4C · Protein HI0227: “Yhch protein (HI0227) copper complex”. X-ray diffraction, 1 ligand (CU), 8 pockets (best druggability 0.70). MolNFT v1 #21256 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1S4C
Type: protein
Length: 592 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein HI0227
UniProt: P44583
Ligands: CU
Pockets: 8 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 13% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein HI0227	protein	150	15% helix, 41% strand	P44583
B	Protein HI0227	protein	155	14% helix, 42% strand	P44583
C	Protein HI0227	protein	147	14% helix, 41% strand	P44583
D	Protein HI0227	protein	140	10% helix, 43% strand	P44583

Ligands and binding sites

CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
ACT · Acetate ion · additive · chains A

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	92	0.70	0.93	38	empty
2	69	0.64	0.92	23	empty
3	305	0.57	0.77	36	empty
4	263	0.55	0.77	31	empty
5	146	0.43	0.75	27	empty

Interfaces

5 interfaces between chains.

B–C · 1071 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 1052 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 236 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 79 Å² buried · 1 hydrogen bond · protein-protein
A–C · 74 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1S4C · Yhch protein (HI0227) copper complex · the same entry in another collection · chain D against D, TM-score 1.00
P44583 · AlphaFold monomer V2.0 prediction for uncharacterized protein HI_0227 (P44583) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P44583
Elsewhere: RCSB PDB 1S4C · PDBe 1S4C · UniProt P44583

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