2H43: Human Fragment D

Crystal Structure of Human Fragment D Complexed with Ala-His-Arg-Pro-amide. Determined by X-ray diffraction at 2.7 Å resolution. Released 5 Dec 2006.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 8
Atoms: 10,770
Mol. weight: 171.05 kDa
Ligands: CA
Released: 5 Dec 2006

Explore 2H43 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2H43 contains 46 α-helices and 96 β-strands across 7 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, 1 β-strand

Element	Residues	Length	Sheet
α-helix	130-159	30
β-strand	165	1	1
α-helix	175-188	14

Chain B: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	167-192	26
β-strand	196	1	1
β-strand	198-199	2	2
α-helix	202	1
β-strand	203-204	2	3
β-strand	208	1	4
α-helix	211-216	6
β-strand	223-227	5	4
β-strand	236-241	6	4
α-helix	244-246	3
β-strand	249-255	7	4
α-helix	266-271	6
β-strand	272-274	3	4
β-strand	277-278	2	5
β-strand	288-289	2	5
β-strand	292-294	3	4
α-helix	296-303	8
β-strand	309-315	7	4
β-strand	321-331	11	4
α-helix	334-336	3
β-strand	340-345	6	4
α-helix	352-355	4
α-helix	363-366	4
β-strand	376	1	6
β-strand	377	1	7
β-strand	380	1	7
β-strand	402	1	6
β-strand	407	1	8
β-strand	410-411	2	9
β-strand	421	1	10
α-helix	424-426	3
β-strand	436-437	2	9
α-helix	438-441	4
β-strand	445	1	10
β-strand	449-455	7	4

Chain C: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	106-134	29
α-helix	138-139	2
β-strand	140-141	2	2
β-strand	150	1	11
α-helix	153-157	5
β-strand	165-169	5	11
β-strand	178-184	7	11
β-strand	190-197	8	11
α-helix	208-213	6
β-strand	215-216	2	11
β-strand	217-218	2	3
β-strand	226-227	2	11
α-helix	230-237	8
β-strand	244-251	8	11
β-strand	257-263	7	11
β-strand	266-267	2	12
α-helix	270-272	3
β-strand	276-277	2	12
β-strand	280-283	4	11
β-strand	291	1	13
α-helix	301-304	4
β-strand	306	1	13
α-helix	310-312	3
β-strand	313-314	2	14
β-strand	317	1	14
α-helix	326-330	5
β-strand	333-334	2	14
β-strand	342-343	2	15
β-strand	353	1	16
α-helix	356-358	3
β-strand	368-369	2	15
β-strand	377	1	16
β-strand	381-388	8	11

Chain D: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	130-132	3
α-helix	134-159	26
β-strand	165	1	17
α-helix	175-190	16

Chain E: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	160-192	33
β-strand	196	1	17
β-strand	198-199	2	18
α-helix	202	1
β-strand	203-204	2	19
β-strand	208	1	20
α-helix	211-216	6
β-strand	223-227	5	20
β-strand	236-241	6	20
α-helix	244-246	3
β-strand	249-255	7	20
α-helix	266-271	6
β-strand	274	1	20
β-strand	277-278	2	21
β-strand	288-289	2	21
β-strand	292-293	2	20
α-helix	296-303	8
β-strand	309-315	7	20
β-strand	321-331	11	20
α-helix	334-336	3
β-strand	340-345	6	20
α-helix	352-355	4
α-helix	363-366	4
β-strand	376	1	22
β-strand	377	1	23
β-strand	380	1	23
β-strand	402	1	22
β-strand	410-411	2	24
β-strand	421	1	25
α-helix	424-426	3
β-strand	436-437	2	24
α-helix	438-441	4
β-strand	445	1	25
β-strand	449-455	7	20

Chain F: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	106-132	27
α-helix	138-139	2
β-strand	140-141	2	18
β-strand	150	1	26
α-helix	153-157	5
β-strand	165-169	5	26
β-strand	178-184	7	26
β-strand	190-197	8	26
α-helix	208-213	6
β-strand	215-216	2	26
β-strand	217-218	2	19
β-strand	226-227	2	26
α-helix	230-237	8
β-strand	244-251	8	26
β-strand	257-262	6	26
β-strand	266-267	2	27
β-strand	276-277	2	27
β-strand	281-283	3	26
β-strand	291	1	28
α-helix	301-304	4
β-strand	306	1	28
α-helix	310-312	3
β-strand	313-314	2	29
β-strand	317	1	29
α-helix	326-329	4
β-strand	333-334	2	29
β-strand	342-343	2	30
β-strand	353	1	31
α-helix	356-358	3
β-strand	368-369	2	30
β-strand	377	1	31
β-strand	381-388	8	26

Chain I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fibrinogen alpha chain	A, D	protein	87	Homo sapiens	P02671 (AlphaFold model)
Fibrinogen beta chain	B, E	protein	328	Homo sapiens	P02675 (AlphaFold model)
Fibrinogen gamma chain	C, F	protein	323	Homo sapiens	P02679 (AlphaFold model)
GLY-HIS-ARG-PRO-AMIDE peptide ligand	I, J	protein	5

Sequence of entity 1 (A, D), FASTA

>2H43_1 Fibrinogen alpha chain (chains A, D)
VSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALA
REVDLKDYEDQQKQLEQVIAKDLLPSR

Sequence of entity 2 (B, E), FASTA

>2H43_2 Fibrinogen beta chain (chains B, E)
DNENVVNEYSSELEKHQLYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQMEYC
RTPCTVSCNIPVVSGKECEEIIRKGGETSEMYLIQPDSSVKPYRVYCDMNTENGGWTVIQ
NRQDGSVDFGRKWDPYKQGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIE
MEDWKGDKVKAHYGGFTVQNEANKYQISVNKYRGTAGNALMDGASQLMGENRTMTIHNGM
FFSTYDRDNDGWLTSDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGGQYTWDMAKHGTDD
GVVWMNWKGSWYSMRKMSMKIRPFFPQQ

Sequence of entity 3 (C, F), FASTA

>2H43_3 Fibrinogen gamma chain (chains C, F)
MLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHDI
TGKDCQDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKNW
IQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKVG
PEADKYRLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCAE
QDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKIIP
FNRLTIGEGQQHHLGGAKQAGDV

Sequence of entity 4 (I, J), FASTA

>2H43_4 GLY-HIS-ARG-PRO-AMIDE peptide ligand (chains I, J)
AHRPX

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6

Primary citation

Differences in Binding Specificity for the Homologous gamma- and beta-Chain "Holes" on Fibrinogen: Exclusive Binding of Ala-His-Arg-Pro-amide by the beta-Chain Hole. Doolittle, R.F., Chen, A., Pandi, L. Biochemistry (2006) 45:13962-13969. DOI 10.1021/bi061219e · PubMed

Other PDB entries of the same protein (UniProt P02671 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5CFA 1.45 Å, Crystal structures of Bbp from Staphylococcus aureus with peptide ligand
4F27 1.92 Å, Crystal structures reveal the multi-ligand binding mechanism of the Staphylococcus…
1FZD 2.1 Å, Structure of recombinant alphaec domain from human fibrinogen-420
1BBR 2.3 Å, The structure of residues 7-16 of the a alpha chain of human fibrinogen bound to bovine…
1FZC 2.3 Å, Crystal structure of fragment double-D from human fibrin with two different bound ligands
3E1I 2.3 Å, Crystal Structure of BbetaD432A Variant Fibrinogen Fragment D with the Peptide Ligand…
2OYH 2.4 Å, Crystal Structure of Fragment D of gammaD298,301A Fibrinogen with the Peptide Ligand…
1RE3 2.45 Å, Crystal Structure of Fragment D of BbetaD398A Fibrinogen with the Peptide Ligand…
1DM4 2.5 Å, SER195ALA mutant of human thrombin complexed with fibrinopeptide a (7-16)
1FPH 2.5 Å, The interaction of thrombin with fibrinogen: a structural basis for its specificity
1FZG 2.5 Å, Crystal structure of fragment D from human fibrinogen with the peptide ligand…
1YCP 2.5 Å, The crystal structure of fibrinogen-aa peptide 1-23 (F8Y) bound to bovine thrombin…

Browse structure collections

About this viewer

MolViewer shows 2H43 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.