MolNFT v1 · #46745 · protein

Methanococcus maripaludis phosphoseryl-tRNA synthetase

2ODR: “Methanococcus maripaludis phosphoseryl-tRNA synthetase”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #46745 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2ODR
Type: protein
Length: 1,858 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoseryl-tRNA synthetase
EC: 6.1.1.-
UniProt: Q6LZE1
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphoseryl-tRNA synthetase (EC 6.1.1.-)	protein	491	38% helix, 23% strand	Q6LZE1
B	Phosphoseryl-tRNA synthetase (EC 6.1.1.-)	protein	448	36% helix, 25% strand	Q6LZE1
C	Phosphoseryl-tRNA synthetase (EC 6.1.1.-)	protein	468	41% helix, 20% strand	Q6LZE1
D	Phosphoseryl-tRNA synthetase (EC 6.1.1.-)	protein	451	41% helix, 20% strand	Q6LZE1

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	170	0.82	0.98	25	empty
2	167	0.82	0.97	25	empty
3	1130	0.78	0.80	94	empty
4	863	0.76	0.80	84	empty
5	1003	0.75	0.78	82	empty

Interfaces

6 interfaces between chains.

C–D · 3252 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 3198 Å² buried · 43 hydrogen bonds · protein-protein
A–D · 2815 Å² buried · 32 hydrogen bonds · protein-protein
B–C · 1987 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 227 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2ODR · Methanococcus Maripaludis Phosphoseryl-tRNA synthetase · the same entry in another collection · chain D against D, TM-score 1.00
Q6LZE1 · AlphaFold monomer V2.0 prediction for O-phosphoserine--TRNA(CYS) ligase (Q6LZE1) · a predicted model of the same protein · chain D against A, TM-score 0.82

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 Q6LZE1
Elsewhere: RCSB PDB 2ODR · PDBe 2ODR · UniProt Q6LZE1

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