SMTL ID : 1lgn.1

DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-pentamer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.58, N.59, E.136, Q.137, D.138 Ligands: D5M.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.58, A:D.58, A:E.136, A:D.138, D5M.3 CA.2: 5 residues within 4Å: Chain A: E.136, D.138, D.145, Q.148 Ligands: D5M.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.136, A:D.138, A:D.138 CA.4: 6 residues within 4Å: Chain B: D.58, N.59, E.136, Q.137, D.138 Ligands: D5M.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.58, B:D.58, B:E.136, B:D.138, D5M.6 CA.5: 5 residues within 4Å: Chain B: E.136, D.138, D.145, Q.148 Ligands: D5M.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.136, B:D.138, B:D.138, B:D.145 CA.7: 6 residues within 4Å: Chain C: D.58, N.59, E.136, Q.137, D.138 Ligands: D5M.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.58, C:D.58, C:E.136, C:D.138, D5M.9 CA.8: 5 residues within 4Å: Chain C: E.136, D.138, D.145, Q.148 Ligands: D5M.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.136, C:D.138, C:D.138 CA.10: 6 residues within 4Å: Chain D: D.58, N.59, E.136, Q.137, D.138 Ligands: D5M.12 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.58, D:D.58, D:E.136, D:D.138, D5M.12 CA.11: 5 residues within 4Å: Chain D: E.136, D.138, D.145, Q.148 Ligands: D5M.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.136, D:D.138, D:D.138 CA.13: 6 residues within 4Å: Chain E: D.58, N.59, E.136, Q.137, D.138 Ligands: D5M.15 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:D.58, E:E.136, E:Q.137, E:D.138, D5M.15 CA.14: 5 residues within 4Å: Chain E: E.136, D.138, D.145, Q.148 Ligands: D5M.15 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.136, E:D.138, E:D.138, E:D.145

5 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

D5M.3: 11 residues within 4Å: Chain A: D.58, N.59, Y.64, Y.74, E.136, D.138, D.145, S.147, Q.148 Ligands: CA.1, CA.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.59, A:Y.74, A:Y.74, A:D.145, A:S.147, A:Q.148 D5M.6: 11 residues within 4Å: Chain B: D.58, N.59, Y.64, Y.74, E.136, D.138, D.145, S.147, Q.148 Ligands: CA.4, CA.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.59, B:Y.74, B:Y.74, B:S.147, B:S.147, B:Q.148 D5M.9: 11 residues within 4Å: Chain C: D.58, N.59, Y.64, Y.74, E.136, D.138, D.145, S.147, Q.148 Ligands: CA.7, CA.8 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.59, C:Y.74, C:Y.74, C:D.145, C:S.147, C:Q.148 D5M.12: 11 residues within 4Å: Chain D: D.58, N.59, Y.64, Y.74, E.136, D.138, D.145, S.147, Q.148 Ligands: CA.10, CA.11 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.59, D:Y.74, D:Y.74, D:D.145, D:S.147, D:Q.148 D5M.15: 11 residues within 4Å: Chain E: D.58, N.59, Y.64, Y.74, E.136, D.138, D.145, S.147, Q.148 Ligands: CA.13, CA.14 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.59, E:Y.74, E:Y.74, E:D.145, E:S.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hohenester, E. et al., Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP. J.Mol.Biol. (1997)

Release Date

1997-12-24

Peptides

SERUM AMYLOID P COMPONENT: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

SERUM AMYLOID P COMPONENT

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