2ZDV: Exploring Thrombin S1 pocket

Exploring Thrombin S1 pocket. Determined by X-ray diffraction at 1.72 Å resolution. Released 28 Oct 2008.

Method: X-ray diffraction
Resolution: 1.72 Å
Organisms: Homo sapiens, Hirudo medicinalis
Chains: 3
Atoms: 2,602
Mol. weight: 35.81 kDa
Ligands: 37U, PO4
Released: 28 Oct 2008

Explore 2ZDV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ZDV contains 16 α-helices and 22 β-strands across 3 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 H: 12 helices, 22 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	56-58	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	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	165-169	5
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 I: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	56-60	5
α-helix	61-63	3

Chain L: 2 helices, 0 β-strands

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin Light Chain	L	protein	36	Homo sapiens	P00734 (AlphaFold model)
Thrombin Heavy Chain	H	protein	259	Homo sapiens	P00734 (AlphaFold model)
Hirudin variant-1	I	protein	11	Hirudo medicinalis	P01050 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>2ZDV_1 Thrombin Light Chain (chains L)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (H), FASTA

>2ZDV_2 Thrombin Heavy Chain (chains H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (I), FASTA

>2ZDV_3 Hirudin variant-1 (chains I)
GDFEEIPEEYL

Ligands and cofactors

ID	Name	Formula	Copies
37U	D-phenylalanyl-N-(3-fluorobenzyl)-L-prolinamide	C21 H24 F N3 O2	1
PO4	Phosphate ion	O4 P	1

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

Primary citation

Exploring Thrombin S1 pocket. Baum, B., Hangauer, D., Heine, A. et al. To be published.

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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