SMTL ID : 1lwu.2 (1 other biounit)

Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x GLY- HIS- ARG- PRO- NH2: Peptide Ligand Gly-His-Arg-Pro-NH2(Non-covalent)

GLY-HIS-ARG-PRO-NH2.1: 13 residues within 4Å: Chain B: 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 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.249 Hydrogen bonds: B:N.228, B:R.270, B:H.272, B:D.296 Salt bridges: B:E.261, B:D.262 GLY-HIS-ARG-PRO-NH2.2: 14 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 Ligands: NDG.12 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:T.232, E:W.249 Hydrogen bonds: E:N.228, E:R.270, E:R.270, E:H.272, E:T.295, E:T.295, E:S.307 Salt bridges: E:E.261, E:D.262

6 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-functional Binders)(Non-covalent)

NDG.3: 1 residues within 4Å: Ligands: MAN.6 No protein-ligand interaction detected (PLIP) NDG.12: 5 residues within 4Å: Chain E: M.225, N.228 Ligands: GLY-HIS-ARG-PRO-NH2.2, GLY-HIS-ARG-PRO-NH2.2, NDG.25 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.228 NDG.13: 2 residues within 4Å: Chain E: N.212 Ligands: MAN.14 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.212 NDG.17: 4 residues within 4Å: Chain E: H.110, G.111 Ligands: MAN.16, GAL.18 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.110 NDG.23: 3 residues within 4Å: Ligands: NAG.4, BMA.5, MAN.24 No protein-ligand interaction detected (PLIP) NDG.25: 2 residues within 4Å: Ligands: NDG.12, BMA.15 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain B: M.225, N.228 Ligands: NDG.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.225, B:N.228 NAG.8: 3 residues within 4Å: Chain C: N.125, T.127 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.125 NAG.9: 2 residues within 4Å: Ligands: NAG.8, MAN.10 No protein-ligand interaction detected (PLIP) NAG.20: 3 residues within 4Å: Chain F: N.125, T.127 Ligands: NAG.21 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.125 NAG.21: 1 residues within 4Å: Ligands: NAG.20 No protein-ligand interaction detected (PLIP)

2 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.5: 3 residues within 4Å: Ligands: MAN.6, NDG.23, MAN.24 No protein-ligand interaction detected (PLIP) BMA.15: 1 residues within 4Å: Ligands: NDG.25 No protein-ligand interaction detected (PLIP)

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

MAN.6: 2 residues within 4Å: Ligands: NDG.3, BMA.5 No protein-ligand interaction detected (PLIP) MAN.10: 1 residues within 4Å: Ligands: NAG.9 No protein-ligand interaction detected (PLIP) MAN.14: 2 residues within 4Å: Ligands: NDG.13, MAN.16 No protein-ligand interaction detected (PLIP) MAN.16: 4 residues within 4Å: Chain E: H.110, Y.187 Ligands: MAN.14, NDG.17 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.110, E:Y.187 MAN.24: 2 residues within 4Å: Ligands: BMA.5, NDG.23 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain B: D.245, D.247, W.249, K.256 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.245, B:D.245, B:D.247, B:W.249, B:K.256 CA.11: 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.19: 4 residues within 4Å: Chain E: D.245, D.247, W.249, K.256 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.245, E:D.245, E:D.247, E:W.249, E:K.256 CA.22: 5 residues within 4Å: Chain F: D.238, D.240, Y.242, E.243, 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

1 x GAL: beta-D-galactopyranose(Non-functional Binders)

GAL.18: 1 residues within 4Å: Ligands: NDG.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide. Biochemistry (2002)

Release Date

2002-08-23

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

D
G

B
E

E
H

C
F

F
I

Fibrinogen alpha-1 chain

Fibrinogen beta chain

Fibrinogen gamma chain

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