MolNFT v1 · #100030 · protein

Crystal structure for the complex of thrombin mutant D102N and hirudin

4MLF: “Crystal structure for the complex of thrombin mutant D102N and hirudin”. X-ray diffraction, 2 ligands (NAG, NA), 4 pockets (best druggability 0.75). MolNFT v1 #100030 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4MLF
Type: protein
Length: 352 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin; Hirudin variant-1
EC: 3.4.21.5
UniProt: P00734, P01050
Ligands: NAG, NA
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thrombin (EC 3.4.21.5)	protein	32	31% helix, 0% strand	P00734
B	Thrombin (EC 3.4.21.5)	protein	259	14% helix, 35% strand	P00734
D	Hirudin variant-1	protein	61	0% helix, 31% strand	P01050

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
NA · Sodium ion · metal · chains B
ACT · Acetate ion · additive · 3 copies · chains B, A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	155	0.75	0.92	27	empty
2	275	0.53	0.75	26	empty
3	83	0.35	0.76	22	empty
4	52	0.27	0.74	16	ACT

Interfaces

2 interfaces between chains.

B–D · 1637 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1174 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

4MLF · Crystal structure for the complex of thrombin mutant D102N and hirudin · the same entry in another collection · chain A against A, TM-score 1.00
P01050 · AlphaFold monomer V2.0 prediction for hirudin variant-1 (P01050) · a predicted model of the same protein · chain D against A, TM-score 0.85

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 P01050
Elsewhere: RCSB PDB 4MLF · PDBe 4MLF · UniProt P00734 · UniProt P01050

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