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Structure of E. COLI MS115-1 HORMA:CDNC:TRIP13 complex

Analyse Structure of E. COLI MS115-1 HORMA:CDNC:TRIP13 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6P8V
Type: protein
Length: 2,265 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATPase, aaa family; E. COLI MS115-1 cdnc; E. COLI MS115-1 horma
UniProt: D7Y2H4, D7Y2H2, A0A1X1LKT4
Ligands: ATP, MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 7 distinct chains · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATPase, aaa family	protein	299	54% helix, 12% strand	D7Y2H4
B	ATPase, aaa family	protein	302	54% helix, 12% strand	D7Y2H4
C, D	ATPase, aaa family	protein	303	54% helix, 12% strand	D7Y2H4
E	ATPase, aaa family	protein	298	53% helix, 13% strand	D7Y2H4
F	ATPase, aaa family	protein	270	55% helix, 12% strand	D7Y2H4
G	E. COLI MS115-1 cdnc	protein	320	50% helix, 13% strand	D7Y2H2
H	E. COLI MS115-1 horma	protein	170	30% helix, 31% strand	A0A1X1LKT4

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains A, B, C, D, E, G
MG · Magnesium ion · metal · chains G

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1051	0.83	0.84	80	ATP, MG
2	690	0.82	0.86	67	ATP
3	609	0.81	0.87	71	empty
4	710	0.81	0.85	82	ATP
5	736	0.80	0.84	81	ATP

Interfaces

17 interfaces between chains.

C–D · 2406 Å² buried · 33 hydrogen bonds · protein-protein
D–E · 2377 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 2347 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 2292 Å² buried · 28 hydrogen bonds · protein-protein
E–F · 1220 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 modified, 1 covalent (engineered, covalent ligand).

Compared structures

6P8V · Structure of E. coli MS115-1 HORMA:CdnC:Trip13 complex · the same entry in another collection · chain H against H, TM-score 1.00
D7Y2H4 · AlphaFold monomer V2.0 prediction for CD-ntase-associated protein 6 (D7Y2H4) · a predicted model of the same protein · chain B against A, TM-score 0.98
D7Y2H2 · AlphaFold monomer V2.0 prediction for cyclic AMP-AMP-AMP synthase (D7Y2H2) · a predicted model of the same protein · chain G against A, TM-score 0.96

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 D7Y2H4
Every structure of UniProt D7Y2H2
Every structure of UniProt A0A1X1LKT4
Elsewhere: RCSB PDB 6P8V · PDBe 6P8V · UniProt D7Y2H4 · UniProt D7Y2H2 · UniProt A0A1X1LKT4

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