MolNFT v1 · #88177 · protein

Chlorobium tepidum ferritin

4CMY: “Chlorobium tepidum ferritin”. X-ray diffraction, 1 ligand (FE), 20 pockets (best druggability 0.77). MolNFT v1 #88177 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4CMY
Type: protein
Length: 3,918 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin
UniProt: Q8KBP5
Ligands: FE
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 80% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E, F, G, H, K, L, M, P, Q, R, T, X	Ferritin	protein	163	80% helix, 2% strand	Q8KBP5
B, I, J, N, O, U, W	Ferritin	protein	164	80% helix, 2% strand	Q8KBP5
S	Ferritin	protein	162	81% helix, 2% strand	Q8KBP5
V	Ferritin	protein	163	80% helix, 2% strand	Q8KBP5

Ligands and binding sites

FE · Fe (III) ion · metal · 48 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	410	0.77	0.86	42	empty
2	376	0.76	0.86	30	empty
3	337	0.75	0.87	28	empty
4	276	0.74	0.88	26	empty
5	413	0.74	0.84	31	empty

Interfaces

66 interfaces between chains.

A–M · 1175 Å² buried · 15 hydrogen bonds · protein-protein
D–F · 1167 Å² buried · 18 hydrogen bonds · protein-protein
C–E · 1158 Å² buried · 17 hydrogen bonds · protein-protein
S–U · 1157 Å² buried · 17 hydrogen bonds · protein-protein
H–P · 1150 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4CMY · Chlorobium tepidum Ferritin · the same entry in another collection · chain A against A, TM-score 1.00

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 Q8KBP5
Elsewhere: RCSB PDB 4CMY · PDBe 4CMY · UniProt Q8KBP5

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