1OOK: Human Alpha Thrombin

Crystal Structure of the Complex of Platelet Receptor GPIb-alpha and Human alpha-Thrombin. Determined by X-ray diffraction at 2.3 Å resolution. Released 22 Jul 2003.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,111
Mol. weight: 67.93 kDa
Ligands: NAG
Released: 22 Jul 2003

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

Secondary structure: helices and β-sheets

1OOK contains 19 α-helices and 42 β-strands across 4 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	8-10	3
α-helix	14C-14H	6

Chain B: 11 helices, 23 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	120-121	2
β-strand	122	1	2
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	2
β-strand	151	1	7
β-strand	154	1	5
β-strand	156-163	8	2
α-helix	165-169	5
α-helix	175-176	2
β-strand	180-183	4	2
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	235-242	8

Chain G: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	8
β-strand	12-16	5	8
β-strand	33-37	5	8
β-strand	45-47	3	9
α-helix	48-51	4
β-strand	59-61	3	8
β-strand	69-71	3	9
β-strand	81-83	3	8
β-strand	104-106	3	8
β-strand	128-130	3	8
α-helix	139-140	2
β-strand	152-154	3	8
β-strand	176-178	3	8
β-strand	199-201	3	8
β-strand	207	1	10
α-helix	214-222	9
α-helix	224-226	3
β-strand	227	1	8
α-helix	243-245	3
β-strand	247	1	11
β-strand	248	1	10
β-strand	255	1	11
α-helix	256-258	3
β-strand	282	1	7

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Human Alpha Thrombin	A	protein	36	Homo sapiens	P00734 (AlphaFold model)
Human Alpha Thrombin	B	protein	259	Homo sapiens	P00734 (AlphaFold model)
PHE-PRO-ARG-Chloromethylketone	P	protein	3
Platelet glycoprotein Ib alpha chain precursor	G	protein	290	Homo sapiens	P07359 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1OOK_1 Human Alpha Thrombin (chains A)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (B), FASTA

>1OOK_2 Human Alpha Thrombin (chains B)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (P), FASTA

>1OOK_3 PHE-PRO-ARG-Chloromethylketone (chains P)
FPR

Sequence of entity 4 (G), FASTA

>1OOK_4 Platelet glycoprotein Ib alpha chain precursor (chains G)
HPICEVSKVASHLEVNCDKRNLTALPPDLPKDTTILHLSENLLYTFSLATLMPYTRLTQL
NLDRAELTKLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGAL
RGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQ
ENSLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQDNAENVYVWKQGVDVKAMT
SNVASVQCDNSDKFPVYKYPGKGCPTLGDEGDTDLYDYYPEEDTEGDKVR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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

Primary citation

Modulation of alpha-thrombin function by distinct interactions with platelet glycoprotein Ibalpha. Celikel, R., McClintock, R.A., Roberts, J.R. et al. Science (2003) 301:218-221. DOI 10.1126/science.1084183 · 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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