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Crystal structure of smap (lsm) protein from methanococcus vannielii

Analyse Crystal structure of smap (lsm) protein from methanococcus vannielii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MKI
Type: protein
Length: 974 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Like-sm ribonucleoprotein core
UniProt: A6UPF5
Ligands: CA
Pockets: 9 · best druggability 0.49

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, F, G, I, J, K, L, M	Like-sm ribonucleoprotein core	protein	70	16% helix, 49% strand	A6UPF5
D	Like-sm ribonucleoprotein core	protein	67	10% helix, 52% strand	A6UPF5
H	Like-sm ribonucleoprotein core	protein	71	11% helix, 48% strand	A6UPF5
N	Like-sm ribonucleoprotein core	protein	66	12% helix, 52% strand	A6UPF5

Ligands and binding sites

CA · Calcium ion · metal · 10 copies · chains C, D, E, F, G, I, J, K, L, M
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains L, M, N

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	117	0.49	0.80	23	empty
2	105	0.45	0.79	19	empty
3	92	0.44	0.79	20	empty
4	66	0.40	0.80	13	empty
5	66	0.39	0.79	15	empty

Interfaces

28 interfaces between chains.

L–M · 842 Å² buried · 13 hydrogen bonds · protein-protein
H–I · 839 Å² buried · 12 hydrogen bonds · protein-protein
F–G · 838 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 838 Å² buried · 14 hydrogen bonds · protein-protein
K–L · 837 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5MKI · Crystal structure of SmAP (LSm) protein from Methanococcus vannielii · 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 A6UPF5
Elsewhere: RCSB PDB 5MKI · PDBe 5MKI · UniProt A6UPF5

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