4CH2: Thrombin, light chain

Low-salt crystal structure of a thrombin-GpIbalpha peptide complex. Determined by X-ray diffraction at 1.6 Å resolution. Released 11 Dec 2013.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: HOMO SAPIENS
Chains: 6
Atoms: 5,406
Mol. weight: 72.95 kDa
Ligands: 0G6
Released: 11 Dec 2013

Explore 4CH2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4CH2 contains 28 α-helices and 52 β-strands across 5 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 A: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	300-302	3
α-helix	309-315	7

Chain B: 12 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	322	1	1
β-strand	325-326	2	2
α-helix	327-328	2
β-strand	335-340	6	3
β-strand	345-352	8	3
β-strand	357-360	4	3
α-helix	362-364	3
β-strand	366-367	2	4
α-helix	368-370	3
β-strand	372-373	2	4
α-helix	376-378	3
β-strand	379-383	5	3
β-strand	387	1	5
β-strand	397-399	3	3
β-strand	401-406	6	3
β-strand	411	1	6
β-strand	417	1	6
β-strand	421-425	5	3
α-helix	428-431	4
β-strand	432	1	7
β-strand	435	1	7
α-helix	437-438	2
β-strand	439	1	2
α-helix	440-441	2
α-helix	443-449	7
β-strand	455-460	6	2
β-strand	469	1	8
β-strand	473	1	8
β-strand	479	1	5
β-strand	481-487	7	2
α-helix	490-495	6
α-helix	500-501	2
β-strand	505-508	4	2
α-helix	512-514	3
β-strand	519	1	1
β-strand	528-532	5	2
β-strand	539-547	9	2
β-strand	558-562	5	2
α-helix	567-576	10

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	300-302	3
α-helix	309-317	9

Chain D: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	322	1	9
β-strand	325-326	2	10
α-helix	327-328	2
β-strand	335-340	6	11
β-strand	345-354	10	11
β-strand	357-360	4	11
α-helix	362-364	3
β-strand	366-367	2	12
α-helix	368-370	3
β-strand	372-373	2	12
α-helix	376-378	3
β-strand	379-383	5	11
β-strand	387	1	13
β-strand	397-399	3	11
β-strand	401-406	6	11
β-strand	411	1	14
β-strand	417	1	14
β-strand	421-425	5	11
α-helix	428-431	4
β-strand	432	1	15
β-strand	435	1	15
α-helix	437-438	2
β-strand	439	1	10
α-helix	440-441	2
α-helix	443-449	7
β-strand	455-460	6	10
β-strand	479	1	13
β-strand	481-487	7	10
α-helix	490-495	6
β-strand	505-508	4	10
β-strand	519	1	9
β-strand	528-532	5	10
β-strand	539-547	9	10
β-strand	558-562	5	10
α-helix	564-566	3
α-helix	567-577	11

Chain Q: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	276-277	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin, light chain	A, C	protein	36	HOMO SAPIENS	P00734 (AlphaFold model)
Thrombin, heavy chain	B, D	protein	259	HOMO SAPIENS	P00734 (AlphaFold model)
Platelet glycoprotein ib alpha chain, residues 287-300	P, Q	protein	14	HOMO SAPIENS	P07359 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4CH2_1 THROMBIN, LIGHT CHAIN (chains A, C)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (B, D), FASTA

>4CH2_2 THROMBIN, HEAVY CHAIN (chains B, D)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (P, Q), FASTA

>4CH2_3 PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300 (chains P, Q)
GDTDLYDYYPEEDT

Ligands and cofactors

ID	Name	Formula	Copies
0G6	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexa…	C21 H34 Cl N6 O3	2

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

Primary citation

Gpibalpha Interacts Exclusively with Exosite II of Thrombin. Lechtenberg, B.C., Freund, S.M.V., Huntington, J.A. J Mol Biol (2014) 426:881. DOI 10.1016/J.JMB.2013.11.027 · 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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