MolNFT v1 · #28065 · protein

Crystal structure of mcsg target APC27401 from shigella flexneri

1Y2I · Hypothetical protein S0862: “Crystal structure of mcsg target APC27401 from shigella flexneri”. X-ray diffraction, 6 pockets (best druggability 0.85). MolNFT v1 #28065 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1Y2I
Type: protein
Length: 545 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein S0862
UniProt: Q83LS2
Pockets: 6 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Hypothetical protein S0862	protein	109	28% helix, 44% strand	Q83LS2

Pockets

6 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	1103	0.85	0.87	97	empty
2	103	0.39	0.75	13	empty
3	105	0.38	0.75	18	empty
4	90	0.36	0.75	14	empty
5	87	0.34	0.74	15	empty

Interfaces

5 interfaces between chains.

D–E · 1468 Å² buried · 28 hydrogen bonds · protein-protein
A–E · 1461 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1448 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1442 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1441 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified (engineered).

Compared structures

1Y2I · Crystal Structure of MCSG Target APC27401 from Shigella flexneri · the same entry in another collection · chain B against B, TM-score 1.00
Q83LS2 · AlphaFold monomer V2.0 prediction for UPF0145 protein ybjq (Q83LS2) · a predicted model of the same protein · chain A against A, TM-score 0.90

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 Q83LS2
Elsewhere: RCSB PDB 1Y2I · PDBe 1Y2I · UniProt Q83LS2

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