SMTL ID : 1lgn.1

DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT

Coordinates

PDB Format

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

DA.11: 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 32 PLIP interactions: 5 interactions with chain E, 6 interactions with chain A, 8 interactions with chain C, 6 interactions with chain D, 7 interactions with chain B Hydrogen bonds: E:N.59, E:Y.74, E:Y.74, E:D.145, E:S.147, A:N.59, A:Y.74, A:Y.74, A:D.145, A:S.147, A:Q.148, C:N.59, C:Y.74, C:Y.74, C:D.138, C:D.138, C:D.145, C:S.147, C:Q.148, D:N.59, D:Y.74, D:Y.74, D:D.145, D:S.147, D:Q.148, B:N.59, B:Y.74, B:Y.74, B:D.138, B:S.147, B:S.147, B:Q.148 DA.12: 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.3, CA.4 Protein-ligand interaction information (PLIP) not available DA.13: 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.5, CA.6 Protein-ligand interaction information (PLIP) not available DA.14: 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.7, CA.8 Protein-ligand interaction information (PLIP) not available DA.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.9, CA.10 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   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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