SMTL ID : 1fzb.1

CRYSTAL STRUCTURE OF CROSSLINKED FRAGMENT D

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x GLY- PRO- ARG- PRO: PEPTIDE LIGAND GPRG(Non-covalent)

GLY-PRO-ARG-PRO.1: 12 residues within 4Å: Chain C: D.210, D.214, T.218, F.235, Q.242, D.243, K.251, C.252, H.253, Y.276, D.277, R.288 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.235 Hydrogen bonds: C:Q.242, C:H.253, C:D.277 Salt bridges: C:D.243, C:K.251 pi-Cation interactions: C:Y.276 GLY-PRO-ARG-PRO.2: 10 residues within 4Å: Chain F: D.214, T.218, F.235, Q.242, D.243, K.251, C.252, H.253, Y.276, D.277 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:T.218, F:F.235 Hydrogen bonds: F:Q.242, F:H.253, F:D.277, F:D.277 Salt bridges: F:D.243, F:K.251

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.3: 2 residues within 4Å: Chain B: E.230, N.231 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.231 NAG.5: 3 residues within 4Å: Chain E: M.228, E.230, N.231 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.230, E:N.231

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain C: D.231, D.233, F.235, G.237, N.238 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.231, C:D.233, C:F.235 CA.6: 6 residues within 4Å: Chain F: D.231, D.233, F.235, E.236, G.237, N.238 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.231, F:D.233, F:F.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spraggon, G. et al., Crystal structures of fragment D from human fibrinogen and its crosslinked counterpart from fibrin. Nature (1997)

Release Date

1997-12-03

Peptides

FIBRINOGEN: AD
FIBRINOGEN: BE
FIBRINOGEN: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

FIBRINOGEN

FIBRINOGEN

FIBRINOGEN

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