MolNFT v1 · #12625 · protein

Histidyl-tRNA synthetase complexed with histidyl-adenylate

1KMM: “Histidyl-tRNA synthetase complexed with histidyl-adenylate”. X-ray diffraction, 1 ligand (HAM), 13 pockets (best druggability 0.82). MolNFT v1 #12625 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KMM
Type: protein
Length: 1,499 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histidyl-tRNA synthetase
EC: 6.1.1.21
UniProt: P60906
Ligands: HAM
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histidyl-tRNA synthetase (EC 6.1.1.21)	protein	386	41% helix, 23% strand	P60906
B	Histidyl-tRNA synthetase (EC 6.1.1.21)	protein	364	39% helix, 24% strand	P60906
C	Histidyl-tRNA synthetase (EC 6.1.1.21)	protein	387	41% helix, 22% strand	P60906
D	Histidyl-tRNA synthetase (EC 6.1.1.21)	protein	362	39% helix, 24% strand	P60906

Ligands and binding sites

HAM · Histidyl-adenosine monophosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	907	0.82	0.84	108	empty
2	950	0.80	0.82	101	empty
3	1156	0.77	0.79	71	empty
4	250	0.70	0.86	38	HAM
5	267	0.69	0.85	40	HAM

Interfaces

6 interfaces between chains.

A–B · 3959 Å² buried · 67 hydrogen bonds · protein-protein
C–D · 3896 Å² buried · 65 hydrogen bonds · protein-protein
B–C · 203 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 135 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 30 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1KMM · Histidyl-tRNA synthetase complexed with histidyl-adenylate · the same entry in another collection · chain D against D, TM-score 1.00
P60906 · AlphaFold monomer V2.0 prediction for histidine--tRNA ligase (P60906) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 P60906
Elsewhere: RCSB PDB 1KMM · PDBe 1KMM · UniProt P60906

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