MolNFT v1 · #165812 · protein

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

6U7B: “Structure of E. COLI MS115-1 CDNC:HORMA-deltan complex”. X-ray diffraction, 3 ligands (AMP, MG, CL), 8 pockets (best druggability 0.79). MolNFT v1 #165812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6U7B
Type: protein
Length: 986 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E. COLI MS115-1 cdnc; BACHORMA_1 domain-containing protein
UniProt: D7Y2H2, A0A1X1LKT4
Ligands: AMP, MG, CL
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 44% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E. COLI MS115-1 cdnc	protein	315	52% helix, 12% strand	D7Y2H2
B	BACHORMA_1 domain-containing protein	protein	176	31% helix, 34% strand	A0A1X1LKT4
C	E. COLI MS115-1 cdnc	protein	320	50% helix, 13% strand	D7Y2H2
D	BACHORMA_1 domain-containing protein	protein	175	29% helix, 34% strand	A0A1X1LKT4

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · chains C
MG · Magnesium ion · metal · 2 copies · chains A, C
CL · Chloride ion · ion · 2 copies · chains A, C
ACT · Acetate ion · additive · 5 copies · chains B, D

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	962	0.79	0.81	108	ACT
2	634	0.74	0.81	46	MG, AMP
3	674	0.70	0.77	56	MG
4	171	0.42	0.74	20	ACT
5	134	0.39	0.74	19	empty

Interfaces

3 interfaces between chains.

B–D · 1994 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 780 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 754 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6U7B · Structure of E. coli MS115-1 CdnC:HORMA-deltaN complex · the same entry in another collection · chain A against A, TM-score 1.00
D7Y2H2 · AlphaFold monomer V2.0 prediction for cyclic AMP-AMP-AMP synthase (D7Y2H2) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 D7Y2H2
Every structure of UniProt A0A1X1LKT4
Elsewhere: RCSB PDB 6U7B · PDBe 6U7B · UniProt D7Y2H2 · UniProt A0A1X1LKT4

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