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Crystal structure of ccmm N-terminal domain in complex with ccmn

Analyse Crystal structure of ccmm N-terminal domain in complex with ccmn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7D6C
Type: protein
Length: 788 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carbon dioxide concentrating mechanism protein ccmm; Carboxysome assembly protein ccmn
UniProt: Q03513, P46204
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 4% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Carbon dioxide concentrating mechanism protein ccmm	protein	167	8% helix, 38% strand	Q03513
2	Carbon dioxide concentrating mechanism protein ccmm	protein	169	9% helix, 37% strand	Q03513
3	Carboxysome assembly protein ccmn	protein	106	0% helix, 49% strand	P46204
4	Carboxysome assembly protein ccmn	protein	104	0% helix, 49% strand	P46204
5	Carboxysome assembly protein ccmn	protein	121	0% helix, 42% strand	P46204
F	Carboxysome assembly protein ccmn	protein	121	0% helix, 40% strand	P46204

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	782	0.79	0.83	88	empty
2	753	0.78	0.82	83	empty
3	138	0.43	0.76	21	empty
4	94	0.41	0.77	16	empty
5	56	0.39	0.81	15	empty

Interfaces

7 interfaces between chains.

2–5 · 1124 Å² buried · 14 hydrogen bonds · protein-protein
1–F · 1066 Å² buried · 12 hydrogen bonds · protein-protein
4–F · 1036 Å² buried · 6 hydrogen bonds · protein-protein
3–5 · 975 Å² buried · 2 hydrogen bonds · protein-protein
3–4 · 561 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7D6C · Crystal structure of CcmM N-terminal domain in complex with CcmN · the same entry in another collection · chain F against F, TM-score 1.00
P46204 · AlphaFold monomer V2.0 prediction for carboxysome assembly protein ccmn (P46204) · a predicted model of the same protein · chain 4 against A, TM-score 0.99
Q03513 · AlphaFold monomer V2.0 prediction for carboxysome assembly protein ccmm (Q03513) · a predicted model of the same protein · chain 1 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 Q03513
Every structure of UniProt P46204
Elsewhere: RCSB PDB 7D6C · PDBe 7D6C · UniProt Q03513 · UniProt P46204

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