MolNFT v1 · #113454 · protein

Thrombin in complex with 3-chloro-benzamide

5AFY · Thrombin heavy chain: “Thrombin in complex with 3-chloro-benzamide”. X-ray diffraction, 5 ligands (WCE, TYS, NAG), 3 pockets (best druggability 0.55). MolNFT v1 #113454 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AFY
Type: protein
Length: 289 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin heavy chain; Hirudin variant-2; Thrombin light chain
EC: 3.4.21.5
UniProt: P00734, P28511
Ligands: WCE, TYS, NAG, NA, PO4
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Thrombin heavy chain (EC 3.4.21.5)	protein	250	15% helix, 36% strand	P00734
I	Hirudin variant-2	protein	11	0% helix, 0% strand	P28511
L	Thrombin light chain (EC 3.4.21.5)	protein	28	36% helix, 0% strand	P00734

Ligands and binding sites

WCE · 3-chloro-benzamide · ligand · chains H
TYS · O-sulfo-L-tyrosine · ligand · chains H, I
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
NA · Sodium ion · metal · 2 copies · chains H
PO4 · Phosphate ion · ion · chains H
DMS · Dimethyl sulfoxide · additive · 2 copies · chains H
GOL · Glycerol · additive · 2 copies · chains H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	238	0.55	0.77	37	WCE
2	63	0.36	0.78	11	TYS
3	56	0.28	0.74	13	GOL

Interfaces

2 interfaces between chains.

H–L · 1123 Å² buried · 27 hydrogen bonds · protein-protein
H–I · 501 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).

Compared structures

5AFY · Thrombin in complex with 3-chloro-benzamide · the same entry in another collection · chain H against H, TM-score 1.00
P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H against A, TM-score 0.93
P28511 · AlphaFold monomer V2.0 prediction for hirudin-3B' (P28511) · a predicted model of the same protein · chain I against A, TM-score 0.47

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
Every structure of UniProt P28511
Elsewhere: RCSB PDB 5AFY · PDBe 5AFY · UniProt P00734 · UniProt P28511

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