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Crystal structure of thrombin in complex with macrocycle X1VE

Analyse Crystal structure of thrombin in complex with macrocycle X1VE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z48
Type: protein
Length: 1,124 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin light chain; Thrombin heavy chain
UniProt: P00734
Ligands: X1V, NA
Pockets: 10 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 17% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	Thrombin light chain	protein	28	36% helix, 0% strand	P00734
H	Thrombin heavy chain	protein	253	15% helix, 36% strand	P00734
B	Thrombin heavy chain	protein	252	15% helix, 35% strand	P00734
C, E	Thrombin light chain	protein	29	38% helix, 0% strand	P00734
D	Thrombin heavy chain	protein	254	16% helix, 35% strand	P00734
F	Thrombin heavy chain	protein	251	16% helix, 36% strand	P00734

Ligands and binding sites

X1V · 5-chloranyl-N-[[(4S,15R)-2,5,13,16-tetrakis(oxidanylidene)-15-propan-2-yl-9,10-dithia-3, 6,14,17-tetrazabicyclo[17.3.1]tricosa-1(22),19(23),20-trien-4-yl]methyl]thiophene-2-carboxamide · ligand · 4 copies · chains H, B, D, F
NA · Sodium ion · metal · 4 copies · chains H, B, D, F

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

Pockets

10 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	1091	0.80	0.81	109	X1V
2	1112	0.74	0.77	71	empty
3	507	0.68	0.79	63	empty
4	377	0.64	0.79	49	empty
5	103	0.60	0.87	24	empty

Interfaces

13 interfaces between chains.

E–F · 1206 Å² buried · 27 hydrogen bonds · protein-protein
L–H · 1200 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1172 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1123 Å² buried · 23 hydrogen bonds · protein-protein
H–F · 617 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

6Z48 · Crystal structure of Thrombin in complex with macrocycle X1vE · the same entry in another collection · chain L against L, 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 P00734
Elsewhere: RCSB PDB 6Z48 · PDBe 6Z48 · UniProt P00734

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