1RE4: Fragment D of BbetaD398A Fibrinogen

Crystal Structure of Fragment D of BbetaD398A Fibrinogen. Determined by X-ray diffraction at 2.7 Å resolution. Released 25 May 2004.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,755
Mol. weight: 158.41 kDa
Ligands: NAG, CA
Released: 25 May 2004

Explore 1RE4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RE4 contains 53 α-helices and 96 β-strands across 6 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	128-159	32
β-strand	165	1	1
α-helix	175-188	14

Chain B: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	157-159	3
α-helix	160-192	33
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
α-helix	244-246	3
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	296-304	9
β-strand	308-315	8	4
β-strand	321-331	11	4
α-helix	334-336	3
β-strand	340-347	8	4
α-helix	363-366	4
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	421	1	9
β-strand	436-437	2	8
α-helix	438-441	4
β-strand	445	1	9
β-strand	449-456	8	4

Chain C: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	103-133	31
α-helix	138-139	2
β-strand	140-141	2	2
β-strand	150	1	10
α-helix	153-159	7
β-strand	165-169	5	10
β-strand	178-184	7	10
β-strand	190-197	8	10
α-helix	208-213	6
β-strand	215-216	2	10
β-strand	217-218	2	3
β-strand	226-227	2	10
α-helix	230-237	8
β-strand	244-251	8	10
β-strand	257-263	7	10
β-strand	266-267	2	11
α-helix	270-272	3
β-strand	276-277	2	11
β-strand	280-281	2	10
α-helix	289-291	3
α-helix	301-304	4
α-helix	310-312	3
β-strand	313	1	12
β-strand	314	1	13
β-strand	317	1	13
α-helix	326-330	5
β-strand	334	1	12
β-strand	342-343	2	14
β-strand	347	1	15
β-strand	353	1	16
α-helix	356-358	3
β-strand	366	1	15
β-strand	368-369	2	14
β-strand	377	1	16
β-strand	381-388	8	10

Chain D: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	130-135	6
α-helix	140-159	20
β-strand	165	1	17
α-helix	175-185	11

Chain E: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	168-192	25
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	273-274	2	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	308-315	8	20
β-strand	321-331	11	20
α-helix	334-336	3
β-strand	340-347	8	20
α-helix	352-355	4
α-helix	362-366	5
α-helix	373-375	3
β-strand	376	1	22
β-strand	377	1	23
β-strand	380	1	23
α-helix	390-392	3
α-helix	399-401	3
β-strand	402	1	22
β-strand	410-411	2	24
β-strand	421	1	25
β-strand	436-437	2	24
α-helix	438-441	4
β-strand	445	1	25
β-strand	449-456	8	20

Chain F: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	104-134	31
α-helix	138-139	2
β-strand	140-141	2	18
β-strand	150	1	26
α-helix	153-158	6
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	257-265	9	26
β-strand	266-267	2	27
α-helix	270-272	3
β-strand	276-277	2	27
β-strand	280-281	2	26
α-helix	289-291	3
α-helix	302-304	3
β-strand	313	1	28
β-strand	314	1	29
β-strand	317	1	29
α-helix	326-330	5
β-strand	334	1	28
β-strand	342-343	2	30
β-strand	347	1	31
β-strand	353	1	32
α-helix	356-358	3
β-strand	366	1	31
β-strand	368-369	2	30
β-strand	377	1	32
β-strand	381-388	8	26
α-helix	389-391	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fibrinogen alpha/alpha-E chain	A, D	protein	66	Homo sapiens	P02671 (AlphaFold model)
Fibrinogen beta chain	B, E	protein	313	Homo sapiens	P02675 (AlphaFold model)
Fibrinogen gamma chain	C, F	protein	311	Homo sapiens	P02679 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>1RE4_1 Fibrinogen alpha/alpha-E chain (chains A, D)
VIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALAREVDLKDYEDQQKQL
EQVIAK

Sequence of entity 2 (B, E), FASTA

>1RE4_2 Fibrinogen beta chain (chains B, E)
HQLYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQMEYCRTPCTVSCNIPVVSG
KECEEIIRKGGETSEMYLIQPDSSVKPYRVYCDMNTENGGWTVIQNRQDGSVDFGRKWDP
YKQGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIEMEDWKGDKVKAHYGG
FTVQNEANKYQISVNKYRGTAGNALMDGASQLMGENRTMTIHNGMFFSTYDRDNDGWLTS
DPRKQCSKEAGGGWWYNRCHAANPNGRYYWGGQYTWDMAKHGTDDGVVWMNWKGSWYSMR
KMSMKIRPFFPQQ

Sequence of entity 3 (C, F), FASTA

>1RE4_3 Fibrinogen gamma chain (chains C, F)
YEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHDITGKDCQD
IANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKNWIQYKEGF
GHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKVGPEADKYR
LTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCAEQDGSGWW
MNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKIIPFNRLTIG
EGQQHHLGGAK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CA	Calcium ion	Ca	6

Primary citation

BbetaGlu397 and BbetaAsp398 but not BbetaAsp432 are required for "B:b" interactions. Kostelansky, M.S., Bolliger-Stucki, B., Betts, L. et al. Biochemistry (2004) 43:2465-2474. DOI 10.1021/bi035996f · 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…

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