MolNFT v1 · #126432 · protein

The structure of the YCF54 protein from synechocystis sp. PCC6803

5M2U: “The structure of the YCF54 protein from synechocystis sp. PCC6803”. X-ray diffraction, 4 pockets (best druggability 0.73). MolNFT v1 #126432 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5M2U
Type: protein
Length: 425 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YCF54
UniProt: P72777
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YCF54	protein	106	42% helix, 27% strand	P72777
B, C	YCF54	protein	107	41% helix, 27% strand	P72777
D	YCF54	protein	105	42% helix, 26% strand	P72777

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	926	0.73	0.77	79	empty
2	53	0.35	0.78	17	empty
3	94	0.34	0.74	17	empty
4	57	0.33	0.78	13	empty

Interfaces

5 interfaces between chains.

A–B · 759 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 551 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 516 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 117 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 26 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5M2U · The Structure of the Ycf54 protein from Synechocystis sp. PCC6803 · the same entry in another collection · chain A against A, TM-score 1.00
P72777 · AlphaFold monomer V2.0 prediction for YCF54-like protein (P72777) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P72777
Elsewhere: RCSB PDB 5M2U · PDBe 5M2U · UniProt P72777

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