MolNFT v1 · #127031 · protein

Crystal structure of smap (lsm) protein from methanococcus vannielii

5MKN · Like-sm ribonucleoprotein core: “Crystal structure of smap (lsm) protein from methanococcus vannielii”. X-ray diffraction, 1 ligand (U5P), 17 pockets (best druggability 0.74). MolNFT v1 #127031 on GenesisL1: 3D structure, binding…

PDB: 5MKN
Type: protein
Length: 1,962 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Like-sm ribonucleoprotein core
UniProt: A6UPF5
Ligands: U5P
Pockets: 17 · best druggability 0.74

Structure

x-ray diffraction · 9 distinct chains · 10% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, H, I, J, K, L, M, O, P, Q, R, T, V, X	Like-sm ribonucleoprotein core	protein	71	10% helix, 49% strand	A6UPF5
G, a	Like-sm ribonucleoprotein core	protein	67	10% helix, 51% strand	A6UPF5
N	Like-sm ribonucleoprotein core	protein	69	10% helix, 49% strand	A6UPF5
U	Like-sm ribonucleoprotein core	protein	66	11% helix, 52% strand	A6UPF5
W	Like-sm ribonucleoprotein core	protein	67	10% helix, 46% strand	A6UPF5
Y	Like-sm ribonucleoprotein core	protein	69	6% helix, 51% strand	A6UPF5
Z	Like-sm ribonucleoprotein core	protein	68	12% helix, 50% strand	A6UPF5
b	Like-sm ribonucleoprotein core	protein	68	10% helix, 49% strand	A6UPF5
d	Like-sm ribonucleoprotein core	protein	72	10% helix, 43% strand	A6UPF5

Ligands and binding sites

U5P · Uridine-5'-monophosphate · ligand · 30 copies · chains A, B, G, C, D, E, F, H, I, N, J, K, L, M, O, P, U, Q, R, d, T, V, W, b, X, Y, Z, a
PG4 · Tetraethylene glycol · additive · 10 copies · chains A, B, T, C, D, Q, R, E, P, G, U, J, K, M, N, W, X, Y, Z, V, b, d

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

Pockets

17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	565	0.74	0.81	65	empty
2	341	0.68	0.82	42	empty
3	684	0.67	0.76	78	PG4
4	263	0.61	0.80	36	empty
5	170	0.45	0.75	24	empty

Interfaces

45 interfaces between chains.

A–B · 892 Å² buried · 13 hydrogen bonds · protein-protein
I–J · 882 Å² buried · 15 hydrogen bonds · protein-protein
V–b · 865 Å² buried · 12 hydrogen bonds · protein-protein
K–L · 865 Å² buried · 14 hydrogen bonds · protein-protein
M–N · 861 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5MKN · Crystal structure of SmAP (LSm) protein from Methanococcus vannielii · the same entry in another collection · chain B against B, 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 5MKN · PDBe 5MKN · UniProt A6UPF5

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