SMTL ID : 1n73.1

Fibrin D-Dimer, Lamprey complexed with the PEPTIDE LIGAND: GLY-HIS-ARG-PRO-AMIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x GLY- HIS- ARG- PRO: peptide ligand: Gly-his-Arg-Pro-amide(Non-covalent)

GLY-HIS-ARG-PRO.1: 11 residues within 4Å: Chain C: F.215, D.221, Y.224, Y.242, Q.249, D.250, R.258, C.259, H.260, Y.283, D.284 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.242, C:Y.242, C:Y.283 Hydrogen bonds: C:Q.249, C:R.258, C:R.258, C:R.258, C:H.260, C:D.284, C:D.284 Salt bridges: C:D.250 GLY-HIS-ARG-PRO.2: 13 residues within 4Å: Chain F: F.215, D.217, D.221, T.225, Y.242, Q.249, D.250, R.258, C.259, H.260, Y.283, D.284, R.295 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:T.225, F:Y.242, F:Y.242 Hydrogen bonds: F:D.217, F:Q.249, F:Q.249, F:R.258, F:R.258, F:H.260, F:D.284, F:R.295 Salt bridges: F:D.250 GLY-HIS-ARG-PRO.3: 13 residues within 4Å: Chain B: N.228, M.231, T.232, W.249, E.261, D.262, R.270, C.271, H.272, T.295, D.296, M.302 Ligands: NAG.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.249 Hydrogen bonds: B:R.270, B:H.272, B:D.296 Salt bridges: B:E.261, B:D.262 GLY-HIS-ARG-PRO.4: 15 residues within 4Å: Chain E: L.224, N.228, M.231, T.232, W.249, E.261, D.262, R.270, C.271, H.272, T.295, D.296, M.302, S.307 Ligands: NAG.9 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:L.224, E:T.232, E:W.249 Hydrogen bonds: E:R.270, E:R.270, E:H.272, E:S.307 Salt bridges: E:E.261, E:D.262 pi-Cation interactions: E:W.249

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

NAG.5: 4 residues within 4Å: Chain B: M.225, G.226, N.228 Ligands: GLY-HIS-ARG-PRO.3 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.225 Hydrogen bonds: B:N.228 NAG.7: 1 residues within 4Å: Chain C: N.125 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.125 NAG.9: 4 residues within 4Å: Chain E: M.225, G.226, N.228 Ligands: GLY-HIS-ARG-PRO.4 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:M.225 Hydrogen bonds: E:N.228 NAG.11: 2 residues within 4Å: Chain F: N.125, T.127 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.125, F:T.127

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain B: D.245, D.247, W.249, N.250, K.256 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.245, B:D.247, B:W.249, B:K.256 CA.8: 5 residues within 4Å: Chain C: D.238, D.240, Y.242, E.243, G.244 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.238, C:D.238, C:D.240, C:Y.242, C:G.244 CA.10: 5 residues within 4Å: Chain E: D.245, D.247, W.249, N.250, K.256 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.245, E:D.247, E:W.249, E:K.256 CA.12: 4 residues within 4Å: Chain F: D.238, D.240, Y.242, G.244 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.238, F:D.238, F:D.240, F:Y.242, F:G.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., The Crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface. Biochemistry (2002)

Release Date

2003-01-07

Peptides

Fibrin alpha-1 chain: AD
Fibrin beta chain: BE
Fibrin gamma chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Fibrin alpha-1 chain

Fibrin beta chain

Fibrin gamma chain

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