SMTL ID : 1fzc.1

CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH TWO DIFFERENT BOUND LIGANDS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x GLY- PRO- ARG- PRO: FIBRIN(Non-covalent)

GLY-PRO-ARG-PRO.1: 13 residues within 4Å: Chain C: F.208, D.210, D.214, T.218, F.235, Q.242, D.243, K.251, C.252, H.253, Y.276, D.277, R.288 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.208, C:F.235, C:K.251 Hydrogen bonds: C:Q.242, C:K.251, C:C.252, C:H.253, C:H.253 Water bridges: C:K.251 Salt bridges: C:D.243 pi-Cation interactions: C:Y.276 GLY-PRO-ARG-PRO.2: 13 residues within 4Å: Chain F: F.208, D.210, D.214, T.218, F.235, Q.242, D.243, K.251, C.252, H.253, Y.276, D.277, R.288 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:F.235, F:K.251 Hydrogen bonds: F:Q.242, F:K.251, F:C.252, F:H.253, F:D.277 Water bridges: F:D.210, F:D.277, F:D.277 Salt bridges: F:D.243 pi-Cation interactions: F:Y.276 GLY-PRO-ARG-PRO.3: 13 residues within 4Å: Chain B: N.231, M.234, T.235, W.252, E.264, D.265, R.273, C.274, H.275, T.298, D.299, M.305 Ligands: NAG-NAG.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.235, B:W.252 Hydrogen bonds: B:R.273, B:R.273, B:C.274, B:H.275, B:T.298, B:D.299 Salt bridges: B:E.264, B:D.265 GLY-PRO-ARG-PRO.4: 14 residues within 4Å: Chain E: L.227, N.231, M.234, T.235, W.252, E.264, D.265, R.273, C.274, H.275, T.298, D.299, M.305 Ligands: NAG.9 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:L.227, E:T.235, E:W.252 Hydrogen bonds: E:R.273, E:R.273, E:C.274, E:H.275, E:D.299 Water bridges: E:D.265, E:D.265, E:S.310 Salt bridges: E:E.264, E:D.265

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.5: 4 residues within 4Å: Chain B: M.228, N.231 Ligands: GLY-HIS-ARG-PRO.3, MAN.6 No protein-ligand interaction detected (PLIP)

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.6: 1 residues within 4Å: Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 3 residues within 4Å: Chain B: D.248, D.250, W.252 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.248, B:D.250, B:W.252, H2O.5, H2O.6 CA.8: 4 residues within 4Å: Chain C: D.231, D.233, F.235, G.237 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.231, C:D.231, C:D.233, C:F.235, C:G.237 CA.10: 3 residues within 4Å: Chain E: D.248, D.250, W.252 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.248, E:D.250, E:W.252, H2O.9 CA.11: 4 residues within 4Å: Chain F: D.231, D.233, F.235, G.237 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.231, F:D.231, F:D.233, F:F.235, F:G.237

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.9: 5 residues within 4Å: Chain E: M.228, N.231 Ligands: GLY-HIS-ARG-PRO.4, GLY-HIS-ARG-PRO.4, NAG.12 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.231 Water bridges: E:M.228 NAG.12: 1 residues within 4Å: Ligands: NAG.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Everse, S.J. et al., Crystal structure of fragment double-D from human fibrin with two different bound ligands. Biochemistry (1998)

Release Date

1998-10-14

Peptides

FIBRIN: AD
FIBRIN: BE
FIBRIN: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

FIBRIN

FIBRIN

FIBRIN

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