MolNFT v1 · #163797 · protein

Crystal structure of bacterial parb dimer bound to cdp

6SDK · Stage 0 sporulation protein J: “Crystal structure of bacterial parb dimer bound to cdp”. X-ray diffraction, 2 ligands (CDP, CA), 12 pockets (best druggability 0.85). MolNFT v1 #163797 on GenesisL1: 3D structure, binding sites and…

PDB: 6SDK
Type: protein
Length: 795 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Stage 0 sporulation protein J
UniProt: P26497
Ligands: CDP, CA
Pockets: 12 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Stage 0 sporulation protein J	protein	199	58% helix, 13% strand	P26497
B	Stage 0 sporulation protein J	protein	198	58% helix, 13% strand	P26497

Ligands and binding sites

CDP · Cytidine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 8 copies · chains A, B, C, D

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

Pockets

12 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	323	0.85	0.95	52	CDP, CA
2	305	0.85	0.96	49	CDP, CA
3	241	0.50	0.75	23	empty
4	137	0.41	0.75	28	empty
5	60	0.40	0.81	13	empty

Interfaces

4 interfaces between chains.

A–B · 2748 Å² buried · 50 hydrogen bonds · protein-protein
C–D · 2713 Å² buried · 44 hydrogen bonds · protein-protein
A–D · 66 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 16 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

6SDK · Crystal structure of bacterial ParB dimer bound to CDP · the same entry in another collection · chain A against A, TM-score 1.00
P26497 · AlphaFold monomer V2.0 prediction for stage 0 sporulation protein J (P26497) · a predicted model of the same protein · chain A against A, TM-score 0.55

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 P26497
Elsewhere: RCSB PDB 6SDK · PDBe 6SDK · UniProt P26497

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