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Crystal structure of the restriction-modification controller protein C.ESP1396I tetramer in complex with its natural 35 base-pair operator

Analyse Crystal structure of the restriction-modification controller protein C.ESP1396I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CLC
Type: protein + DNA
Length: 376 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Regulatory protein; 35-mer
UniProt: Q8GGH0
Ligands: MG
Pockets: 8 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 71% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Regulatory protein	protein	76	72% helix, 1% strand	Q8GGH0
B, C	Regulatory protein	protein	77	69% helix, 1% strand	Q8GGH0
E	35-mer	dna	35	—	—
F	35-mer	dna	35	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains B, E, C, F

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

Pockets

8 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	172	0.60	0.83	27	empty
2	91	0.37	0.76	14	empty
3	97	0.36	0.75	14	empty
4	78	0.35	0.77	17	empty
5	76	0.35	0.77	16	empty

Interfaces

12 interfaces between chains.

E–F · 1607 Å² buried · 140 hydrogen bonds · nucleic-nucleic
C–D · 992 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 980 Å² buried · 16 hydrogen bonds · protein-protein
D–F · 411 Å² buried · 12 hydrogen bonds · protein-nucleic
A–E · 409 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

3CLC · Crystal Structure of the Restriction-Modification Controller Protein C.Esp1396I Tetramer… · 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 Q8GGH0
Elsewhere: RCSB PDB 3CLC · PDBe 3CLC · UniProt Q8GGH0

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