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Crystal structure of cupin fold protein STHE2323 from sphaerobacter thermophilus

Analyse Crystal structure of cupin fold protein STHE2323 from sphaerobacter thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4E2G
Type: protein
Length: 931 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cupin 2 conserved barrel domain protein
UniProt: D1C798
Ligands: NI, K
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, F, G, H	Cupin 2 conserved barrel domain protein	protein	115	10% helix, 52% strand	D1C798
B	Cupin 2 conserved barrel domain protein	protein	114	7% helix, 53% strand	D1C798
C	Cupin 2 conserved barrel domain protein	protein	126	13% helix, 48% strand	D1C798
D	Cupin 2 conserved barrel domain protein	protein	116	10% helix, 52% strand	D1C798

Ligands and binding sites

NI · Nickel (II) ion · metal · 4 copies · chains B, C, F, G
K · Potassium ion · metal · 2 copies · chains C, D, G, H
ACT · Acetate ion · additive · chains F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1101	0.76	0.79	92	empty
2	84	0.76	0.98	24	ACT
3	84	0.73	0.96	23	NI
4	742	0.68	0.75	62	K, NI
5	631	0.67	0.76	63	empty

Interfaces

15 interfaces between chains.

G–H · 1569 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1562 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1527 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1512 Å² buried · 25 hydrogen bonds · protein-protein
F–H · 826 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 49 modified (engineered).

Compared structures

4E2G · Crystal structure of Cupin fold protein Sthe2323 from Sphaerobacter thermophilus · 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
Every structure of UniProt D1C798
Elsewhere: RCSB PDB 4E2G · PDBe 4E2G · UniProt D1C798

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