MolNFT v1 · #111513 · protein

Hmd II from methanocaldococcus jannaschii

4YT2 · H(2)-forming methylenetetrahydromethanopterin…: “Hmd II from methanocaldococcus jannaschii”. X-ray diffraction, 11 pockets (best druggability 0.82). MolNFT v1 #111513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YT2
Type: protein
Length: 689 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
UniProt: Q58734
Pockets: 11 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338	protein	343	55% helix, 11% strand	Q58734
B	H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338	protein	346	55% helix, 11% strand	Q58734

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
PGE · Triethylene glycol · additive · chains A

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	147	0.82	0.97	29	empty
2	298	0.75	0.87	48	PEG
3	69	0.60	0.90	21	empty
4	69	0.54	0.87	20	empty
5	194	0.53	0.78	22	empty

Interfaces

1 interface between chains.

A–B · 6021 Å² buried · 55 hydrogen bonds · protein-protein

Compared structures

4YT2 · Hmd II from Methanocaldococcus jannaschii · the same entry in another collection · chain A against A, TM-score 1.00
Q58734 · AlphaFold monomer V2.0 prediction for H(2)-forming methylenetetrahydromethanopterin… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q58734
Elsewhere: RCSB PDB 4YT2 · PDBe 4YT2 · UniProt Q58734

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.