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High pH structure of RTMS5 H146S variant

Analyse High pH structure of RTMS5 H146S variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P4M
Type: protein
Length: 1,744 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GFP-like non-fluorescent chromoprotein
UniProt: P83690
Ligands: CRQ, IOD
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	GFP-like non-fluorescent chromoprotein	protein	218	5% helix, 57% strand	P83690

Ligands and binding sites

CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
IOD · Iodide ion · ion · 24 copies · chains A, C, B, D, G, E, F, H

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	832	0.80	0.83	109	IOD
2	1195	0.79	0.81	112	IOD
3	82	0.75	0.98	28	CRQ
4	80	0.75	0.98	30	CRQ
5	82	0.74	0.97	31	CRQ

Interfaces

9 interfaces between chains.

E–F · 1288 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1283 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 1279 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1273 Å² buried · 19 hydrogen bonds · protein-protein
F–H · 859 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 cofactor (chromophore).

Compared structures

2P4M · High pH structure of Rtms5 H146S variant · the same entry in another collection · chain H against H, TM-score 1.00
P83690 · AlphaFold monomer V2.0 prediction for GFP-like non-fluorescent chromoprotein (P83690) · a predicted model of the same protein · 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 P83690
Elsewhere: RCSB PDB 2P4M · PDBe 2P4M · UniProt P83690

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