MolNFT v1 · #61495 · protein

Carboxysome subunit, CCMK1 C-terminal deletion mutant

3DN9: “Carboxysome subunit, CCMK1 C-terminal deletion mutant”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.46). MolNFT v1 #61495 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3DN9
Type: protein
Length: 534 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CCMK1 C-terminal deletion mutant
UniProt: P72760
Ligands: SO4
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	CCMK1 C-terminal deletion mutant	protein	88	41% helix, 36% strand	P72760
B, D, F	CCMK1 C-terminal deletion mutant	protein	90	36% helix, 39% strand	P72760

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, F, B, C, D, E

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	208	0.46	0.74	24	SO4

Interfaces

6 interfaces between chains.

A–B · 1013 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1012 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1009 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 972 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 966 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3DN9 · Carboxysome Subunit, CcmK1 C-terminal deletion mutant · the same entry in another collection · chain F against F, TM-score 1.00
P72760 · AlphaFold monomer V2.0 prediction for carboxysome shell protein CCMK1 (P72760) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P72760
Elsewhere: RCSB PDB 3DN9 · PDBe 3DN9 · UniProt P72760

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