1DX5: Thrombin-thrombomodulin complex

Crystal structure of the thrombin-thrombomodulin complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 10 Apr 2000.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 12
Atoms: 14,018
Mol. weight: 194.11 kDa
Ligands: 0GJ, NAG, CA
Released: 10 Apr 2000

Explore 1DX5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1DX5 contains 64 α-helices and 140 β-strands across 12 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 D: 2 helices, 0 β-strands

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

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

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14C-14H	6

Chain I: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	350-353	4
β-strand	359-362	4	1
β-strand	368-371	4	1
β-strand	376-379	4	2
β-strand	382-388	7	2
β-strand	394-396	3	3
β-strand	398-399	2	4
β-strand	407-408	2	4
β-strand	413-416	4	3
β-strand	420-423	4	3
α-helix	426-429	4
β-strand	436-439	4	5
β-strand	444-448	5	5
β-strand	455-458	4	5

Chain J: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	350-353	4
β-strand	359-362	4	6
β-strand	368-371	4	6
β-strand	376-379	4	7
β-strand	382-388	7	7
β-strand	394-396	3	8
β-strand	398-399	2	9
β-strand	407-408	2	9
β-strand	413-416	4	8
β-strand	420-423	4	8
α-helix	426-429	4
β-strand	436-439	4	10
β-strand	444-447	4	10
β-strand	456-458	3	10

Chain K: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	350-353	4
β-strand	359-362	4	11
β-strand	368-371	4	11
β-strand	376-379	4	12
β-strand	382-388	7	12
β-strand	394-396	3	13
β-strand	398-400	3	14
β-strand	406-408	3	14
β-strand	413-416	4	13
β-strand	420-423	4	13
α-helix	426-429	4
β-strand	436-439	4	15
β-strand	444-447	4	15
β-strand	456-458	3	15

Chain L: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	350-353	4
β-strand	359-362	4	16
β-strand	368-371	4	16
β-strand	376-379	4	17
β-strand	382-388	7	17
β-strand	394-396	3	18
β-strand	398-400	3	19
β-strand	406-408	3	19
β-strand	413-416	4	18
β-strand	420-423	4	18
α-helix	426-429	4
β-strand	436-439	4	20
β-strand	444-447	4	20
β-strand	457-458	2	20

Chain M: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	21
β-strand	20-21	2	22
α-helix	22-23	2
β-strand	30-35	6	23
β-strand	39-46	8	23
β-strand	51-54	4	23
α-helix	56-58	3
β-strand	60-60A	2	24
α-helix	60B-60D	3
β-strand	60F-60G	2	24
α-helix	61-63	3
β-strand	64-68	5	23
β-strand	72	1	25
β-strand	81-83	3	23
β-strand	85-90	6	23
β-strand	95	1	26
β-strand	100	1	26
β-strand	104-108	5	23
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	22
α-helix	126-129C	7
β-strand	135-140	6	22
β-strand	154	1	25
β-strand	156-162	7	22
α-helix	165-170	6
α-helix	175-177	3
β-strand	180-183	4	22
α-helix	186-186B	3
β-strand	189	1	21
β-strand	198-202	5	22
β-strand	207-215	9	22
β-strand	226-230	5	22
α-helix	232-234	3
α-helix	235-244	10

Chain N: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	27
β-strand	20-21	2	28
α-helix	22-23	2
β-strand	30-35	6	29
β-strand	39-46	8	29
β-strand	51-54	4	29
α-helix	56-58	3
β-strand	60-60A	2	30
α-helix	60B-60D	3
β-strand	60F-60G	2	30
α-helix	61-63	3
β-strand	64-68	5	29
β-strand	72	1	31
β-strand	81-83	3	29
β-strand	85-90	6	29
β-strand	95	1	32
β-strand	100	1	32
β-strand	104-108	5	29
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	28
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	28
β-strand	154	1	31
β-strand	156-162	7	28
α-helix	165-170	6
α-helix	175-176	2
β-strand	180-183	4	28
α-helix	186-186B	3
β-strand	189	1	27
β-strand	198-202	5	28
β-strand	207-215	9	28
β-strand	226-230	5	28
α-helix	232-234	3
α-helix	235-244	10

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin light chain	A, B, C, D	protein	36	Homo sapiens	P00734 (AlphaFold model)
Thrombomodulin	I, J, K, L	protein	118	Homo sapiens	P07204 (AlphaFold model)
Thrombin heavy chain	M, N, O, P	protein	259	Homo sapiens	P00734 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>1DX5_1 Thrombin light chain (chains A, B, C, D)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (I, J, K, L), FASTA

>1DX5_2 Thrombomodulin (chains I, J, K, L)
VEPVDPCFRANCEYQCQPLDQTSYLCVCAEGFAPIPHEPHRCQMFCNQTACPADCDPNTQ
ASCECPEGYILDDGFICTDIDECENGGFCSGVCHNLPGTFECICGPDSALAGQIGTDC

Sequence of entity 3 (M, N, O, P), FASTA

>1DX5_3 Thrombin heavy chain (chains M, N, O, P)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFIENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Ligands and cofactors

ID	Name	Formula	Copies
0GJ	L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydr…	C14 H28 Cl N6 O5	16
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
CA	Calcium ion	Ca	4

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

Primary citation

Structural Basis for the Anticoagulant Activity of the Thrombin-Thrombomodulin Complex. Fuentes-Prior, P., Iwanaga, Y., Huber, R. et al. Nature (2000) 404:518. DOI 10.1038/35006683 · 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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