4DT7: Thrombin

Crystal structure of thrombin bound to the activation domain QEDQVDPRLIDGKMTRRGDS of protein C. Determined by X-ray diffraction at 1.9 Å resolution. Released 9 May 2012.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,080
Mol. weight: 71.85 kDa
Released: 9 May 2012

Explore 4DT7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DT7 contains 28 α-helices and 45 β-strands across 6 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.

Chains A and C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14C-14K	9

Chain B: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-36	7	3
β-strand	38-46	9	3
β-strand	51-54	4	3
α-helix	56-59	4
β-strand	60-60A	2	4
α-helix	60B-60D	3
β-strand	60F-60G	2	4
α-helix	61-63	3
β-strand	65-68	4	3
β-strand	72	1	5
β-strand	81-90	10	3
β-strand	104-108	5	3
α-helix	111-114	4
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
β-strand	180-183	4	2
α-helix	186-186B	3
β-strand	189	1	1
β-strand	198-202	5	2
β-strand	207-216	10	2
β-strand	226-230	5	2
α-helix	232-234	3
α-helix	235-245	11

Chain D: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	6
β-strand	20-21	2	7
α-helix	22-23	2
β-strand	30-35	6	8
β-strand	39-46	8	8
β-strand	51-54	4	8
α-helix	56-58	3
β-strand	60-60A	2	9
α-helix	60B-60D	3
β-strand	60F-60G	2	9
α-helix	61-63	3
β-strand	64-68	5	8
β-strand	72	1	10
β-strand	81-83	3	8
β-strand	85-90	6	8
β-strand	95	1	11
β-strand	100	1	11
β-strand	104-108	5	8
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	7
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	7
β-strand	154	1	10
β-strand	156-162	7	7
α-helix	165-170	6
β-strand	180-183	4	7
α-helix	186-186B	3
β-strand	189	1	6
β-strand	198-202	5	7
β-strand	207-216	10	7
β-strand	226-230	5	7
α-helix	232-234	3
α-helix	235-244	10

Chains E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	39-40	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin light chain	A, C	protein	32	Homo sapiens	P00734 (AlphaFold model)
Thrombin heavy chain	B, D	protein	259	Homo sapiens	P00734 (AlphaFold model)
Vitamin K-dependent protein C	E, F	protein	20	Homo sapiens	P04070 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4DT7_1 Thrombin light chain (chains A, C)
GEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (B, D), FASTA

>4DT7_2 Thrombin heavy chain (chains B, D)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (E, F), FASTA

>4DT7_3 Vitamin K-dependent protein C (chains E, F)
QEDQVDPRLIDGKMTRRGDS

Primary citation

Exposure of R169 controls protein C activation and autoactivation. Pozzi, N., Barranco-Medina, S., Chen, Z. et al. Blood (2012) 120:664-670. DOI 10.1182/blood-2012-03-415323 · PubMed

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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