3GIS: Na-free Thrombin

Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin. Determined by X-ray diffraction at 2.4 Å resolution. Released 18 Aug 2009.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 9
Atoms: 10,192
Mol. weight: 146.57 kDa
Ligands: CA
Released: 18 Aug 2009

Explore 3GIS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3GIS contains 49 α-helices and 101 β-strands across 9 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, C and E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	1J-1G	4
α-helix	1C-1A	3
α-helix	8-10	3
α-helix	14C-14H	6

Chains B and D: 11 helices, 21 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	56-59	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	64-68	5	3
β-strand	72	1	5
β-strand	81-83	3	3
β-strand	85-90	6	3
β-strand	104-108	5	3
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	2
α-helix	126-129C	7
β-strand	135-140	6	2
β-strand	154	1	5
β-strand	156-162	7	2
α-helix	165-171	7
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 F: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	11
β-strand	20-21	2	12
α-helix	22-23	2
β-strand	30-35	6	13
β-strand	39-46	8	13
β-strand	51-54	4	13
α-helix	56-59	4
β-strand	60-60A	2	14
β-strand	60F-60G	2	14
α-helix	61-63	3
β-strand	64-68	5	13
β-strand	72	1	15
β-strand	81-83	3	13
β-strand	85-90	6	13
β-strand	95	1	16
β-strand	100	1	16
β-strand	104-108	5	13
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	12
α-helix	126-129C	7
β-strand	135-140	6	12
β-strand	154	1	15
β-strand	156-162	7	12
α-helix	165-171	7
β-strand	180-183	4	12
α-helix	186-186B	3
β-strand	189	1	11
β-strand	198-202	5	12
β-strand	207-215	9	12
β-strand	226-230	5	12
α-helix	232-234	3
α-helix	235-242	8

Chain X: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	359-362	4	17
β-strand	368-371	4	17
β-strand	376-379	4	18
β-strand	382-388	7	18
β-strand	394-396	3	19
β-strand	398	1	20
β-strand	408	1	20
β-strand	413-416	4	19
β-strand	420-423	4	19
α-helix	424	1
α-helix	426-429	4
β-strand	436-440	5	21
β-strand	443-448	6	21
β-strand	449-450	2	22
β-strand	455-458	4	21

Chain Y: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	359-362	4	23
β-strand	368-371	4	23
β-strand	376-379	4	24
β-strand	382-388	7	24
β-strand	394-396	3	25
β-strand	413-416	4	25
β-strand	420-423	4	25
α-helix	426-429	4
β-strand	436-439	4	26
β-strand	444-447	4	26
β-strand	457-458	2	26

Chain Z: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	359-362	4	27
β-strand	368-371	4	27
β-strand	376-378	3	28
β-strand	386-388	3	28
β-strand	394-396	3	29
β-strand	398-399	2	30
β-strand	407-408	2	30
β-strand	413-416	4	29
β-strand	420-423	4	29
α-helix	424	1
α-helix	426-429	4
β-strand	436-440	5	22
β-strand	443-448	6	22
β-strand	449-450	2	21
β-strand	455-458	4	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prothrombin	A, C, E	protein	49	Homo sapiens	P00734 (AlphaFold model)
Prothrombin	B, D, F	protein	259	Homo sapiens	P00734 (AlphaFold model)
Thrombomodulin	X, Y, Z	protein	121	Homo sapiens	P07204 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>3GIS_1 Prothrombin (chains A, C, E)
TATSEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (B, D, F), FASTA

>3GIS_2 Prothrombin (chains B, D, F)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (X, Y, Z), FASTA

>3GIS_3 Thrombomodulin (chains X, Y, Z)
VEPVDPCFRANCEYQCQPLNQTSYLCVCAEGFAPIPHEPHRCQLFCNQTACPADCDPNTQ
ASCECPEGYILDDGFICTDIDECENGGFCSGVCHNLPGTFECICGPDSALAGQIGTDCDS
G

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Water and common crystallization additives (SO4) are not listed.

Primary citation

Molecular basis of thrombomodulin activation of slow thrombin. Adams, T.E., Li, W., Huntington, J.A. J Thromb Haemost (2009) 7:1688-1695. DOI 10.1111/j.1538-7836.2009.03563.x · 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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