Research workbench

Cocrystal structure of the intermembrane space region of the plastid division proteins PARC6 and PDV1

Analyse Cocrystal structure of the intermembrane space region of the plastid division… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5U9O
Type: protein
Length: 1,145 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1
UniProt: Q8VY16, Q9FK13
Pockets: 9 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 29% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	145	28% helix, 38% strand	Q8VY16, Q9FK13
B	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	144	28% helix, 43% strand	Q8VY16, Q9FK13
C	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	145	29% helix, 39% strand	Q8VY16, Q9FK13
D	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	146	29% helix, 40% strand	Q8VY16, Q9FK13
E	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	144	27% helix, 38% strand	Q8VY16, Q9FK13
F	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	142	30% helix, 39% strand	Q8VY16, Q9FK13
G	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	139	29% helix, 43% strand	Q8VY16, Q9FK13
H	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	140	28% helix, 37% strand	Q8VY16, Q9FK13

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	909	0.82	0.84	79	empty
2	211	0.73	0.89	30	empty
3	431	0.70	0.81	44	empty
4	312	0.66	0.82	40	empty
5	191	0.60	0.82	27	empty

Interfaces

14 interfaces between chains.

E–H · 1061 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1048 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 732 Å² buried · 5 hydrogen bonds · protein-protein
A–H · 690 Å² buried · 12 hydrogen bonds · protein-protein
A–G · 576 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5U9O · Cocrystal structure of the intermembrane space region of the plastid division proteins… · the same entry in another collection · chain B against B, TM-score 1.00
Q8VY16 · AlphaFold monomer V2.0 prediction for plastid division protein CDP1, chloroplastic… · a predicted model of the same protein · chain G against A, TM-score 0.91

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 5U9O · PDBe 5U9O · UniProt Q8VY16 · UniProt Q9FK13

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