MolNFT v1 · #100798 · protein

Ccml from thermosynechococcus elongatus bp-1

4N8F · Carbon dioxide concentrating mechanism protein: “Ccml from thermosynechococcus elongatus bp-1”. X-ray diffraction, 2 ligands (MG, SO4), 4 pockets (best druggability 0.71). MolNFT v1 #100798 on GenesisL1: 3D structure, binding sites…

PDB: 4N8F
Type: protein
Length: 477 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carbon dioxide concentrating mechanism protein
UniProt: Q8DKB4
Ligands: MG, SO4
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E	Carbon dioxide concentrating mechanism protein	protein	95	9% helix, 49% strand	Q8DKB4
C	Carbon dioxide concentrating mechanism protein	protein	97	12% helix, 52% strand	Q8DKB4

Ligands and binding sites

MG · Magnesium ion · metal · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E

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

Pockets

4 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	681	0.71	0.79	50	SO4
2	170	0.60	0.83	35	empty
3	101	0.54	0.84	22	empty
4	64	0.47	0.84	19	empty

Interfaces

5 interfaces between chains.

A–E · 1294 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 1281 Å² buried · 30 hydrogen bonds · protein-protein
D–E · 1217 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 1214 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 1214 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

4N8F · CcmL from Thermosynechococcus elongatus BP-1 · the same entry in another collection · chain E against E, TM-score 1.00
Q8DKB4 · AlphaFold monomer V2.0 prediction for carboxysome shell vertex protein ccml (Q8DKB4) · a predicted model of the same protein · chain E against A, TM-score 0.95

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 Q8DKB4
Elsewhere: RCSB PDB 4N8F · PDBe 4N8F · UniProt Q8DKB4

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