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Structure of slyd from thermus thermophilus in complex with S2-W23A peptide

Analyse Structure of slyd from thermus thermophilus in complex with S2-W23A peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ODM
Type: protein
Length: 688 residues
Chains: 13
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidyl-prolyl cis-trans isomerase slyd; 30S ribosomal protein S2
EC: 5.2.1.8
UniProt: Q5SLE7, P0A7V0
Ligands: NH2, CL
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 11 distinct chains · 13% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Peptidyl-prolyl cis-trans isomerase slyd (EC 5.2.1.8)	protein	150	15% helix, 45% strand	Q5SLE7
B	Peptidyl-prolyl cis-trans isomerase slyd (EC 5.2.1.8)	protein	149	15% helix, 46% strand	Q5SLE7
C	Peptidyl-prolyl cis-trans isomerase slyd (EC 5.2.1.8)	protein	153	14% helix, 44% strand	Q5SLE7
E	30S ribosomal protein S2	protein	10	0% helix, 10% strand	P0A7V0
F, H	30S ribosomal protein S2	protein	10	0% helix, 10% strand	P0A7V0
G	30S ribosomal protein S2	protein	6	0% helix, 17% strand	P0A7V0
I	30S ribosomal protein S2	protein	12	0% helix, 8% strand	P0A7V0
J	30S ribosomal protein S2	protein	9	0% helix, 11% strand	P0A7V0
K	30S ribosomal protein S2	protein	14	0% helix, 7% strand	P0A7V0
L	30S ribosomal protein S2	protein	11	0% helix, 18% strand	P0A7V0
M	30S ribosomal protein S2	protein	4	0% helix, 0% strand	P0A7V0

Ligands and binding sites

NH2 · Amino group · ion · 5 copies · chains B, F, A, H, D, I, K, L
CL · Chloride ion · ion · 4 copies · chains A, E, B, G, C, I, D, K
GOL · Glycerol · additive · 2 copies · chains A, E, D
ACT · Acetate ion · additive · chains A

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	727	0.74	0.79	61	empty
2	256	0.63	0.81	41	NH2, CL
3	454	0.59	0.75	48	empty
4	450	0.58	0.74	48	empty
5	220	0.56	0.78	30	empty

Interfaces

23 interfaces between chains.

D–K · 789 Å² buried · 12 hydrogen bonds · protein-protein
C–I · 692 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 661 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 650 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 608 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4ODM · Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide · 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 Q5SLE7
Every structure of UniProt P0A7V0
Elsewhere: RCSB PDB 4ODM · PDBe 4ODM · UniProt Q5SLE7 · UniProt P0A7V0

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