2HLO: Fragment D-dimer from Human Fibrin

Crystal Structure of Fragment D-dimer from Human Fibrin Complexed with Gly-hydroxyPro-Arg-Pro-amide. Determined by X-ray diffraction at 2.6 Å resolution. Released 17 Jul 2007.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 8
Atoms: 10,750
Mol. weight: 171.27 kDa
Ligands: CA
Released: 17 Jul 2007

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

Secondary structure: helices and β-sheets

2HLO contains 52 α-helices and 104 β-strands across 8 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: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	130-160	31
α-helix	161-163	3
β-strand	165	1	1
α-helix	175-188	14

Chain B: 11 helices, 25 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
α-helix	234-235	2
β-strand	236-241	6	4
β-strand	249-255	7	4
α-helix	266-271	6
β-strand	273-274	2	4
β-strand	277-278	2	5
β-strand	288-289	2	5
β-strand	292-293	2	4
α-helix	296-303	8
β-strand	308-315	8	4
β-strand	321-331	11	4
β-strand	340-347	8	4
α-helix	352-355	4
α-helix	362-366	5
α-helix	373-375	3
β-strand	376	1	6
β-strand	377	1	7
β-strand	380	1	7
α-helix	399-401	3
β-strand	402	1	6
β-strand	410-411	2	8
β-strand	415	1	9
β-strand	421	1	10
β-strand	434	1	9
β-strand	436-437	2	8
α-helix	438-441	4
β-strand	445	1	10
β-strand	449-456	8	4

Chain C: 12 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	104-116	13
α-helix	119-134	16
α-helix	139	1
β-strand	140-141	2	2
β-strand	149-150	2	11
α-helix	153-158	6
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	214-216	3	11
β-strand	217-218	2	3
β-strand	226-228	3	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	280-281	2	11
α-helix	289-291	3
α-helix	301-304	4
α-helix	310-312	3
β-strand	313	1	13
β-strand	314	1	14
β-strand	317	1	14
α-helix	326-329	4
β-strand	334	1	13
β-strand	339	1	15
β-strand	342-343	2	16
β-strand	347	1	17
β-strand	353	1	18
β-strand	366	1	17
β-strand	368-369	2	16
β-strand	377	1	18
β-strand	381-388	8	11
α-helix	389-391	3

Chain D: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	136-141	6
α-helix	142-159	18
β-strand	165	1	19
α-helix	178-184	7

Chain E: 12 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	168-192	25
β-strand	196	1	19
β-strand	198-199	2	20
α-helix	202	1
β-strand	203-204	2	21
β-strand	208	1	22
α-helix	211-216	6
β-strand	223-227	5	22
α-helix	234-235	2
β-strand	236-241	6	22
α-helix	244-246	3
β-strand	249-255	7	22
α-helix	266-271	6
β-strand	273-274	2	22
β-strand	277-278	2	23
β-strand	288-289	2	23
β-strand	292-293	2	22
α-helix	296-303	8
β-strand	308-315	8	22
β-strand	321-331	11	22
β-strand	340-347	8	22
α-helix	352-355	4
α-helix	363-366	4
β-strand	376	1	24
β-strand	377	1	25
β-strand	380	1	25
α-helix	399-401	3
β-strand	402	1	24
β-strand	410-411	2	26
β-strand	415	1	27
β-strand	421	1	28
α-helix	424-426	3
β-strand	434	1	27
β-strand	436-437	2	26
α-helix	438-441	4
β-strand	445	1	28
β-strand	449-456	8	22

Chain F: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	112-134	23
α-helix	138-139	2
β-strand	140-141	2	20
β-strand	145-150	6	29
α-helix	153-157	5
β-strand	165-169	5	29
β-strand	178-184	7	29
β-strand	190-197	8	29
α-helix	208-213	6
β-strand	214-216	3	29
β-strand	217-218	2	21
β-strand	226-228	3	29
α-helix	230-237	8
β-strand	244-251	8	29
β-strand	257-263	7	29
β-strand	266-267	2	30
α-helix	270-272	3
β-strand	276-277	2	30
β-strand	280-281	2	29
α-helix	301-304	4
α-helix	310-312	3
β-strand	313	1	31
β-strand	314	1	32
β-strand	317	1	32
α-helix	326-330	5
β-strand	334	1	31
β-strand	339	1	33
β-strand	342	1	34
β-strand	347	1	35
β-strand	353	1	36
α-helix	356-358	3
β-strand	366	1	35
β-strand	369	1	34
β-strand	377	1	36
β-strand	381-388	8	29
α-helix	389-391	3

Chains G and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	15

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)
Isoform Gamma-A of Fibrinogen gamma chain	C, F	protein	324	Homo sapiens	P02679 (AlphaFold model)
Gly-hyp-arg-pro-amide peptide ligand	G, H	protein	5

Sequence of entity 1 (A, D), FASTA

>2HLO_1 Fibrinogen alpha chain (chains A, D)
VSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALA
REVDLKDYEDQQKQLEQVIAKDLLPSR

Sequence of entity 2 (B, E), FASTA

>2HLO_2 Fibrinogen beta chain (chains B, E)
DNENVVNEYSSELEKHQLYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQMEYC
RTPCTVSCNIPVVSGKECEEIIRKGGETSEMYLIQPDSSVKPYRVYCDMNTENGGWTVIQ
NRQDGSVDFGRKWDPYKQGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIE
MEDWKGDKVKAHYGGFTVQNEANKYQISVNKYRGTAGNALMDGASQLMGENRTMTIHNGM
FFSTYDRDNDGWLTSDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGGQYTWDMAKHGTDD
GVVWMNWKGSWYSMRKMSMKIRPFFPQQ

Sequence of entity 3 (C, F), FASTA

>2HLO_3 Isoform Gamma-A of Fibrinogen gamma chain (chains C, F)
KMLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHD
ITGKDCQDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKN
WIQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKV
GPEADKYRLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCA
EQDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKII
PFNRLTIGEGQQHHLGGAKQAGDV

Sequence of entity 4 (G, H), FASTA

>2HLO_4 GLY-HYP-ARG-PRO-AMIDE PEPTIDE LIGAND (chains G, H)
GPRPX

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	7

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

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