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Scaffoldin conformation and dynamics revealed by a ternary complex from the clostridium thermocellum cellulosome

Analyse Scaffoldin conformation and dynamics revealed by a ternary complex from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FL4
Type: protein
Length: 2,156 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycoside hydrolase family 9; Scaffolding dockerin binding protein a; Cellulosome…
UniProt: D1NID1, P71143, C7HJU1
Ligands: CA, SO4
Pockets: 10 · best druggability 0.54

Structure

x-ray diffraction · 9 distinct chains · 16% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycoside hydrolase family 9	protein	68	44% helix, 0% strand	D1NID1
B, E, H	Scaffolding dockerin binding protein a	protein	165	7% helix, 42% strand	P71143
C, F	Cellulosome anchoring protein cohesin region	protein	308	11% helix, 46% strand	C7HJU1
D	Glycoside hydrolase family 9	protein	65	45% helix, 0% strand	D1NID1
G	Glycoside hydrolase family 9	protein	67	39% helix, 0% strand	D1NID1
I	Cellulosome anchoring protein cohesin region	protein	309	12% helix, 46% strand	C7HJU1
J	Glycoside hydrolase family 9	protein	66	41% helix, 0% strand	D1NID1
K	Scaffolding dockerin binding protein a	protein	164	6% helix, 41% strand	P71143
L	Cellulosome anchoring protein cohesin region	protein	306	11% helix, 46% strand	C7HJU1

Ligands and binding sites

CA · Calcium ion · metal · 16 copies · chains A, C, D, F, G, I, J, L
SO4 · Sulfate ion · ion · 58 copies · chains B, C, H, E, F, D, I, K, L

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

Pockets

10 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	138	0.54	0.82	29	empty
2	328	0.54	0.74	38	empty
3	315	0.53	0.75	48	empty
4	130	0.52	0.81	29	empty
5	120	0.48	0.79	25	empty

Interfaces

14 interfaces between chains.

A–C · 866 Å² buried · 18 hydrogen bonds · protein-protein
K–L · 862 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 860 Å² buried · 11 hydrogen bonds · protein-protein
H–I · 849 Å² buried · 11 hydrogen bonds · protein-protein
D–F · 846 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4FL4 · Scaffoldin conformation and dynamics revealed by a ternary complex from the Clostridium… · 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 D1NID1
Every structure of UniProt P71143
Every structure of UniProt C7HJU1
Elsewhere: RCSB PDB 4FL4 · PDBe 4FL4 · UniProt D1NID1 · UniProt P71143 · UniProt C7HJU1

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