MolNFT v1 · #9698 · protein

Crystal structure of an sm-like protein (af-SM1) from archaeoglobus fulgidus at 2.5A resolution

1I4K · Putative snrnp sm-like protein: “Crystal structure of an sm-like protein (af-SM1) from archaeoglobus fulgidus at 2.5A resolution”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #9698 on GenesisL1: 3D structure…

PDB: 1I4K
Type: protein
Length: 2,001 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative snrnp sm-like protein
UniProt: O29386
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 13% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, G, R	Putative snrnp sm-like protein	protein	72	13% helix, 58% strand	O29386
B, D, K, M, P, 1, 2	Putative snrnp sm-like protein	protein	72	13% helix, 58% strand	O29386
C, F, H, J, L, N, O, Q, S, T, U, V, W, X, Y, Z	Putative snrnp sm-like protein	protein	71	14% helix, 58% strand	O29386
I	Putative snrnp sm-like protein	protein	73	12% helix, 58% strand	O29386

Ligands and binding sites

CIT · Citric acid · additive · 2 copies · chains F, G, K, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1147	0.83	0.84	124	empty
2	792	0.81	0.84	95	empty
3	221	0.68	0.86	35	empty
4	558	0.61	0.74	55	CIT
5	146	0.59	0.84	25	empty

Interfaces

57 interfaces between chains.

V–2 · 954 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 946 Å² buried · 9 hydrogen bonds · protein-protein
I–J · 943 Å² buried · 12 hydrogen bonds · protein-protein
H–N · 914 Å² buried · 13 hydrogen bonds · protein-protein
1–2 · 901 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

1I4K · Crystal structure of an sm-like protein (af-SM1) from archaeoglobus fulgidus at 2.5A… · the same entry in another collection · chain K against K, 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 O29386
Elsewhere: RCSB PDB 1I4K · PDBe 1I4K · UniProt O29386

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