MolNFT v1 · #21472 · protein

X-ray structure of YDII_ECOLI northeast structural genomics consortium target ER29.

1SBK · Hypothetical protein ydii: “X-ray structure of YDII_ECOLI northeast structural genomics consortium target ER29.”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.77). MolNFT v1 #21472 on GenesisL1: 3D structure…

PDB: 1SBK
Type: protein
Length: 552 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein ydii
UniProt: P77781
Ligands: SO4
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Hypothetical protein ydii	protein	138	22% helix, 41% strand	P77781

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

4 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	351	0.77	0.87	46	SO4
2	493	0.76	0.83	53	SO4
3	459	0.74	0.83	54	SO4
4	355	0.73	0.84	46	SO4

Interfaces

6 interfaces between chains.

B–D · 1285 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1259 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 563 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 553 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 352 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

1SBK · X-ray structure of YDII_ECOLI northeast structural genomics consortium target ER29. · the same entry in another collection · chain A against A, TM-score 1.00
P77781 · AlphaFold monomer V2.0 prediction for 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (P77781) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P77781
Elsewhere: RCSB PDB 1SBK · PDBe 1SBK · UniProt P77781

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