MolNFT v1 · #141425 · protein

Crystal structure of ccpc regulatory domain in complex with citrate from bacillus amyloliquefaciens

5Z72: “Crystal structure of ccpc regulatory domain in complex with citrate from bacillus amyloliquefaciens”. X-ray diffraction, 1 ligand (NA), 13 pockets (best druggability 0.77). MolNFT v1 #141425 on GenesisL1: 3D structure, binding sites…

PDB: 5Z72
Type: protein
Length: 963 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ccpc
UniProt: A7Z428
Ligands: NA
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Ccpc	protein	197	37% helix, 28% strand	A7Z428
D	Ccpc	protein	193	38% helix, 27% strand	A7Z428
E	Ccpc	protein	179	30% helix, 31% strand	A7Z428

Ligands and binding sites

NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E
FLC · Citrate anion · additive · 5 copies · chains A, B, C, D, E

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1170	0.77	0.79	103	empty
2	64	0.67	0.95	17	NA, FLC
3	66	0.66	0.94	17	NA, FLC
4	69	0.66	0.93	18	FLC
5	64	0.66	0.94	15	FLC

Interfaces

6 interfaces between chains.

A–C · 1280 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 1274 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 678 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 446 Å² buried · 8 hydrogen bonds · protein-protein
C–E · 192 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5Z72 · Crystal structure of CcpC regulatory domain in complex with citrate from Bacillus… · 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 A7Z428
Elsewhere: RCSB PDB 5Z72 · PDBe 5Z72 · UniProt A7Z428

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