MolNFT v1 · #154082 · protein

Structure of the intermembrane space region of PARC6-PDV1

6JZN · Plastid division protein CDP1, chloroplastic: “Structure of the intermembrane space region of PARC6-PDV1”. X-ray diffraction, 5 pockets (best druggability 0.71). MolNFT v1 #154082 on GenesisL1: 3D structure, binding sites and…

PDB: 6JZN
Type: protein
Length: 563 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plastid division protein CDP1, chloroplastic; Peptide from plastid division protein PDV1
UniProt: Q8VY16, Q9FK13
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 6 distinct chains · 31% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Plastid division protein CDP1, chloroplastic	protein	133	32% helix, 46% strand	Q8VY16
B	Plastid division protein CDP1, chloroplastic	protein	134	31% helix, 46% strand	Q8VY16
D	Plastid division protein CDP1, chloroplastic	protein	129	30% helix, 45% strand	Q8VY16
A	Plastid division protein CDP1, chloroplastic	protein	130	29% helix, 47% strand	Q8VY16
G, F, E	Peptide from plastid division protein PDV1	protein	9	44% helix, 0% strand	Q9FK13
H	Peptide from plastid division protein PDV1	protein	10	40% helix, 0% strand	Q9FK13

Pockets

5 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	756	0.71	0.77	57	empty
2	464	0.70	0.80	52	empty
3	69	0.50	0.85	17	empty
4	57	0.47	0.85	17	empty
5	129	0.43	0.76	19	empty

Interfaces

9 interfaces between chains.

B–A · 930 Å² buried · 5 hydrogen bonds · protein-protein
C–G · 653 Å² buried · 7 hydrogen bonds · protein-protein
D–H · 651 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 644 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 602 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6JZN · Structure of the intermembrane space region of PARC6-PDV1 · the same entry in another collection · chain E against E, TM-score 1.00
Q8VY16 · AlphaFold monomer V2.0 prediction for plastid division protein CDP1, chloroplastic… · 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 Q8VY16
Every structure of UniProt Q9FK13
Elsewhere: RCSB PDB 6JZN · PDBe 6JZN · UniProt Q8VY16 · UniProt Q9FK13

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