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Crystal structure of tetrameric tim from pyrococcus woesei.

Analyse Crystal structure of tetrameric tim from pyrococcus woesei. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1HG3
Type: protein
Length: 1,792 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Triosephosphate isomerase
EC: 5.3.1.1
UniProt: P95583
Ligands: 3PP
Pockets: 7 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Triosephosphate isomerase (EC 5.3.1.1)	protein	224	42% helix, 17% strand	P95583

Ligands and binding sites

3PP · 3-phosphonopropanoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

7 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	308	0.64	0.80	43	empty
2	291	0.63	0.80	45	empty
3	282	0.62	0.80	40	empty
4	302	0.61	0.79	44	empty
5	79	0.31	0.73	14	empty

Interfaces

9 interfaces between chains.

G–H · 1431 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 1427 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1424 Å² buried · 34 hydrogen bonds · protein-protein
E–F · 1424 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 749 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1HG3 · Crystal structure of tetrameric TIM from Pyrococcus woesei. · the same entry in another collection · 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 P95583
Elsewhere: RCSB PDB 1HG3 · PDBe 1HG3 · UniProt P95583

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