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Structure of xenopus laevis CRL2LRR1 (state 1)

Analyse Structure of xenopus laevis CRL2LRR1 (state 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SHK
Type: protein
Length: 1,299 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CULLIN_2 domain-containing protein; TCEB2-prov protein; Elongin-C; LRR1; Ring-type…
UniProt: A0A1L8FVB6, Q6PHL7, Q6PHW7, A4QNS4, A0A1L8GNG7
Ligands: ZN
Pockets: 11 · best druggability 0.79

Structure

electron microscopy · 5 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CULLIN_2 domain-containing protein	protein	744	65% helix, 6% strand	A0A1L8FVB6
B	TCEB2-prov protein	protein	97	19% helix, 27% strand	Q6PHL7
C	Elongin-C	protein	98	39% helix, 13% strand	Q6PHW7
L	LRR1	protein	282	21% helix, 21% strand	A4QNS4
R	Ring-type domain-containing protein	protein	78	10% helix, 38% strand	A0A1L8GNG7

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains L, R

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	227	0.79	0.92	26	empty
2	976	0.73	0.76	84	empty
3	423	0.63	0.77	50	empty
4	475	0.61	0.75	47	empty
5	281	0.56	0.77	32	empty

Interfaces

5 interfaces between chains.

A–R · 1834 Å² buried · 36 hydrogen bonds · protein-protein
A–C · 1074 Å² buried · 14 hydrogen bonds · protein-protein
A–L · 1053 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 1038 Å² buried · 7 hydrogen bonds · protein-protein
C–L · 857 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7SHK · Structure of Xenopus laevis CRL2Lrr1 (State 1) · 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 A0A1L8FVB6
Every structure of UniProt Q6PHL7
Every structure of UniProt Q6PHW7
Every structure of UniProt A4QNS4
Every structure of UniProt A0A1L8GNG7
Elsewhere: RCSB PDB 7SHK · PDBe 7SHK · UniProt A0A1L8FVB6 · UniProt Q6PHL7 · UniProt Q6PHW7 · UniProt A4QNS4 · UniProt A0A1L8GNG7

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