6FJT: 4-chloro-benzamidine

4-chloro-benzamidine in complex with thrombin. Determined by X-ray diffraction at 1.27 Å resolution. Released 6 Feb 2019.

Method: X-ray diffraction
Resolution: 1.27 Å
Organisms: Homo sapiens, Hirudo medicinalis
Chains: 3
Atoms: 2,749
Mol. weight: 34.55 kDa
Ligands: DKQ, PO4, NAG
Released: 6 Feb 2019

Explore 6FJT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FJT contains 17 α-helices and 24 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain H: 13 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-46	8	3
β-strand	51-54	4	3
α-helix	56-58	3
β-strand	60-60A	2	4
α-helix	60B-60D	3
β-strand	60F-60G	2	4
α-helix	61-63	3
β-strand	64-68	5	3
β-strand	72	1	5
β-strand	81-90	10	3
β-strand	95	1	6
β-strand	100	1	6
β-strand	104-108	5	3
α-helix	111-114	4
β-strand	115	1	7
β-strand	118	1	7
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-125	3
α-helix	126-129C	7
β-strand	135-140	6	2
β-strand	154	1	5
β-strand	156-162	7	2
α-helix	165-170	6
α-helix	175-176	2
β-strand	180-183	4	2
α-helix	186-186B	3
β-strand	189	1	1
β-strand	198-202	5	2
β-strand	207-215	9	2
β-strand	226-230	5	2
α-helix	232-234	3
α-helix	235-245	11

Chain I: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	519-523	5
α-helix	524-526	3

Chain L: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14C-14I	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prothrombin	L	protein	28	Homo sapiens	P00734 (AlphaFold model)
Prothrombin	H	protein	251	Homo sapiens	P00734 (AlphaFold model)
Hirudin variant-2	I	protein	11	Hirudo medicinalis

Sequence of entity 1 (L), FASTA

>6FJT_1 Prothrombin (chains L)
EADCGLRPLFEKKSLEDKTERELLESYI

Sequence of entity 2 (H), FASTA

>6FJT_2 Prothrombin (chains H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFC
AGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLK
KWIQKVIDQFG

Sequence of entity 3 (I), FASTA

>6FJT_3 Hirudin variant-2 (chains I)
DFEEIPEEYLQ

Ligands and cofactors

ID	Name	Formula	Copies
DKQ	4-chloranylbenzenecarboximidamide	C7 H7 Cl N2	1
PO4	Phosphate ion	O4 P	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (NA, DMS, GOL) are not listed.

Primary citation

4-chloro-benzamidine in complex with thrombin. Abazi, A., Heine, A., Klebe, G. To be published.

Other PDB entries of the same protein (UniProt P00734 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5AFY 1.12 Å, Thrombin in complex with 3-chloro-benzamide
4UD9 1.12 Å, Thrombin in complex with 5-chlorothiophene-2-carboxamide
4UE7 1.13 Å, Thrombin in complex with 1-amidinopiperidine
4UDW 1.16 Å, Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2,…
4UEH 1.16 Å, Thrombin in complex with benzamidine
5AF9 1.18 Å, Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide
3RM2 1.23 Å, Human Thrombin in complex with MI003
5AHG 1.24 Å, Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine
2BVR 1.25 Å, Human thrombin complexed with fragment-based small molecules occupying the S1 pocket
3VXE 1.25 Å, Human alpha-thrombin-Bivalirudin complex at PD5.0
2UUF 1.26 Å, Thrombin-hirugen binary complex at 1.26A resolution
3SI4 1.27 Å, Human Thrombin In Complex With UBTHR104

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