SMTL ID : 3flp.1

Crystal structure of native heptameric SAP-like pentraxin from Limulus polyphemus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-14-mer

Ligands

28 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:E.145, A:Q.146, A:D.147, H2O.1 CA.2: 5 residues within 4Å: Chain A: E.145, D.147, E.154, E.157 Ligands: CA.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.145, A:E.154, A:E.157, H2O.1, H2O.3 CA.3: 6 residues within 4Å: Chain B: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.59, B:E.145, B:E.145, B:Q.146, B:D.147 CA.4: 5 residues within 4Å: Chain B: E.145, D.147, E.154, E.157 Ligands: CA.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.145, B:D.147, B:E.154, B:E.157, H2O.4 CA.5: 6 residues within 4Å: Chain C: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.6 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.59, C:E.145, C:Q.146, C:D.147, H2O.7 CA.6: 5 residues within 4Å: Chain C: E.145, D.147, E.154, E.157 Ligands: CA.5 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.145, C:E.154, C:E.157, H2O.8, H2O.8 CA.7: 6 residues within 4Å: Chain D: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.8 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.59, D:E.145, D:Q.146, D:D.147, H2O.11 CA.8: 5 residues within 4Å: Chain D: E.145, D.147, E.154, E.157 Ligands: CA.7 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.145, D:E.154, D:E.157, H2O.9, H2O.11 CA.9: 6 residues within 4Å: Chain E: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.10 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.59, E:E.145, E:Q.146, E:D.147, H2O.12 CA.10: 5 residues within 4Å: Chain E: E.145, D.147, E.154, E.157 Ligands: CA.9 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.145, E:D.147, E:E.154, E:E.157, H2O.13 CA.11: 6 residues within 4Å: Chain F: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.12 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.59, F:E.145, F:Q.146, F:D.147, H2O.16 CA.12: 5 residues within 4Å: Chain F: E.145, D.147, E.154, E.157 Ligands: CA.11 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.145, F:D.147, F:E.154, F:E.157, H2O.15 CA.13: 6 residues within 4Å: Chain G: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.14 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.59, G:E.145, G:Q.146, G:D.147, H2O.18 CA.14: 5 residues within 4Å: Chain G: E.145, D.147, E.154, E.157 Ligands: CA.13 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.145, G:D.147, G:E.154, G:E.157, H2O.17 CA.15: 6 residues within 4Å: Chain H: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.16 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.59, H:E.145, H:E.145, H:Q.146, H:D.147 CA.16: 5 residues within 4Å: Chain H: E.145, D.147, E.154, E.157 Ligands: CA.15 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.145, H:D.147, H:E.154, H:E.157, H2O.20 CA.17: 6 residues within 4Å: Chain I: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.18 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.59, I:E.145, I:E.145, I:Q.146, I:D.147 CA.18: 5 residues within 4Å: Chain I: E.145, D.147, E.154, E.157 Ligands: CA.17 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.145, I:D.147, I:E.154, I:E.157, H2O.23 CA.19: 6 residues within 4Å: Chain J: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.20 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.59, J:E.145, J:Q.146, J:D.147, H2O.25 CA.20: 5 residues within 4Å: Chain J: E.145, D.147, E.154, E.157 Ligands: CA.19 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.145, J:D.147, J:E.154, J:E.157, H2O.24 CA.21: 6 residues within 4Å: Chain K: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:D.59, K:E.145, K:E.145, K:Q.146, K:D.147 CA.22: 5 residues within 4Å: Chain K: E.145, D.147, E.154, E.157 Ligands: CA.21 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.145, K:D.147, K:E.154, K:E.157, H2O.26 CA.23: 6 residues within 4Å: Chain L: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.24 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:D.59, L:E.145, L:E.145, L:Q.146, L:D.147 CA.24: 5 residues within 4Å: Chain L: E.145, D.147, E.154, E.157 Ligands: CA.23 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.145, L:D.147, L:D.147, L:E.154, L:E.157 CA.25: 6 residues within 4Å: Chain M: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.26 5 PLIP interactions: 4 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:D.59, M:E.145, M:Q.146, M:D.147, H2O.31 CA.26: 5 residues within 4Å: Chain M: E.145, D.147, E.154, E.157 Ligands: CA.25 5 PLIP interactions: 4 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.145, M:D.147, M:E.154, M:E.157, H2O.31 CA.27: 6 residues within 4Å: Chain N: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.28 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:D.59, N:E.145, N:E.145, N:Q.146, N:D.147 CA.28: 5 residues within 4Å: Chain N: E.145, D.147, E.154, E.157 Ligands: CA.27 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:E.145, N:D.147, N:D.147, N:E.154, N:E.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shrive, A.K. et al., Crystal structures of Limulus SAP-like pentraxin reveal two molecular aggregations. J.Mol.Biol. (2009)

Release Date

2009-01-20

Peptides

SAP-like pentraxin: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

SAP-like pentraxin

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