SMTL ID : 3flt.1

Crystal structure of PE-bound octameric SAP-like pentraxin from Limulus polyphemus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-16-mer

Ligands

48 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.2, OPE.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.59, A:E.145, A:E.145, A:Q.146, A:D.147 CA.2: 7 residues within 4Å: Chain A: E.145, D.147, E.154, E.157 Ligands: CA.1, CA.3, OPE.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.145, A:D.147, A:D.147, A:E.154, A:E.157 CA.3: 4 residues within 4Å: Chain A: E.154, E.157 Ligands: CA.2, OPE.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.154 CA.5: 7 residues within 4Å: Chain B: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.6, OPE.8 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.6: 7 residues within 4Å: Chain B: E.145, D.147, E.154, E.157 Ligands: CA.5, CA.7, OPE.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.145, B:D.147, B:D.147, B:E.157 CA.7: 4 residues within 4Å: Chain B: E.154, E.157 Ligands: CA.6, OPE.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.154, B:E.154, B:E.157 CA.9: 7 residues within 4Å: Chain C: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.10, OPE.12 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.59, C:E.145, C:E.145, C:Q.146, C:D.147 CA.10: 7 residues within 4Å: Chain C: E.145, D.147, E.154, E.157 Ligands: CA.9, CA.11, OPE.12 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.145, C:D.147, C:D.147, C:E.154, C:E.157 CA.11: 4 residues within 4Å: Chain C: E.154, E.157 Ligands: CA.10, OPE.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.154 CA.13: 7 residues within 4Å: Chain D: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.14, OPE.16 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.59, D:E.145, D:E.145, D:Q.146, D:D.147 CA.14: 7 residues within 4Å: Chain D: E.145, D.147, E.154, E.157 Ligands: CA.13, CA.15, OPE.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.145, D:D.147, D:D.147, D:E.157 CA.15: 4 residues within 4Å: Chain D: E.154, E.157 Ligands: CA.14, OPE.16 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.154, D:E.154, D:E.157 CA.17: 7 residues within 4Å: Chain E: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.18, OPE.20 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.59, E:E.145, E:E.145, E:Q.146, E:D.147 CA.18: 7 residues within 4Å: Chain E: E.145, D.147, E.154, E.157 Ligands: CA.17, CA.19, OPE.20 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.145, E:D.147, E:D.147, E:E.154, E:E.157 CA.19: 4 residues within 4Å: Chain E: E.154, E.157 Ligands: CA.18, OPE.20 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.154 CA.21: 7 residues within 4Å: Chain F: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.22, OPE.24 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.59, F:E.145, F:E.145, F:Q.146, F:D.147 CA.22: 7 residues within 4Å: Chain F: E.145, D.147, E.154, E.157 Ligands: CA.21, CA.23, OPE.24 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.145, F:D.147, F:D.147, F:E.157 CA.23: 4 residues within 4Å: Chain F: E.154, E.157 Ligands: CA.22, OPE.24 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.154, F:E.154, F:E.157 CA.25: 7 residues within 4Å: Chain G: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.26, OPE.28 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.59, G:E.145, G:E.145, G:Q.146, G:D.147 CA.26: 7 residues within 4Å: Chain G: E.145, D.147, E.154, E.157 Ligands: CA.25, CA.27, OPE.28 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.145, G:D.147, G:D.147, G:E.154, G:E.157 CA.27: 4 residues within 4Å: Chain G: E.154, E.157 Ligands: CA.26, OPE.28 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.154 CA.29: 7 residues within 4Å: Chain H: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.30, OPE.32 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.30: 7 residues within 4Å: Chain H: E.145, D.147, E.154, E.157 Ligands: CA.29, CA.31, OPE.32 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.145, H:D.147, H:D.147, H:E.157 CA.31: 4 residues within 4Å: Chain H: E.154, E.157 Ligands: CA.30, OPE.32 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.154, H:E.154, H:E.157 CA.33: 7 residues within 4Å: Chain I: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.34, OPE.36 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.34: 7 residues within 4Å: Chain I: E.145, D.147, E.154, E.157 Ligands: CA.33, CA.35, OPE.36 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.145, I:D.147, I:D.147, I:E.154, I:E.157 CA.35: 4 residues within 4Å: Chain I: E.154, E.157 Ligands: CA.34, OPE.36 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:E.154 CA.37: 7 residues within 4Å: Chain J: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.38, OPE.40 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:D.59, J:E.145, J:E.145, J:Q.146, J:D.147 CA.38: 7 residues within 4Å: Chain J: E.145, D.147, E.154, E.157 Ligands: CA.37, CA.39, OPE.40 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.145, J:D.147, J:D.147, J:E.157 CA.39: 4 residues within 4Å: Chain J: E.154, E.157 Ligands: CA.38, OPE.40 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.154, J:E.154, J:E.157 CA.41: 7 residues within 4Å: Chain K: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.42, OPE.44 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.42: 7 residues within 4Å: Chain K: E.145, D.147, E.154, E.157 Ligands: CA.41, CA.43, OPE.44 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:E.145, K:D.147, K:D.147, K:E.154, K:E.157 CA.43: 4 residues within 4Å: Chain K: E.154, E.157 Ligands: CA.42, OPE.44 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.154 CA.45: 7 residues within 4Å: Chain L: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.46, OPE.48 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.46: 7 residues within 4Å: Chain L: E.145, D.147, E.154, E.157 Ligands: CA.45, CA.47, OPE.48 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:E.145, L:D.147, L:D.147, L:E.157 CA.47: 4 residues within 4Å: Chain L: E.154, E.157 Ligands: CA.46, OPE.48 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.154, L:E.154, L:E.157 CA.49: 7 residues within 4Å: Chain M: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.50, OPE.52 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:D.59, M:E.145, M:E.145, M:Q.146, M:D.147 CA.50: 7 residues within 4Å: Chain M: E.145, D.147, E.154, E.157 Ligands: CA.49, CA.51, OPE.52 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.145, M:D.147, M:D.147, M:E.154, M:E.157 CA.51: 4 residues within 4Å: Chain M: E.154, E.157 Ligands: CA.50, OPE.52 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:E.154 CA.53: 7 residues within 4Å: Chain N: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.54, OPE.56 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.54: 7 residues within 4Å: Chain N: E.145, D.147, E.154, E.157 Ligands: CA.53, CA.55, OPE.56 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:E.145, N:D.147, N:D.147, N:E.157 CA.55: 4 residues within 4Å: Chain N: E.154, E.157 Ligands: CA.54, OPE.56 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:E.154, N:E.154, N:E.157 CA.57: 7 residues within 4Å: Chain O: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.58, OPE.60 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:D.59, O:E.145, O:E.145, O:Q.146, O:D.147 CA.58: 7 residues within 4Å: Chain O: E.145, D.147, E.154, E.157 Ligands: CA.57, CA.59, OPE.60 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.145, O:D.147, O:D.147, O:E.154, O:E.157 CA.59: 4 residues within 4Å: Chain O: E.154, E.157 Ligands: CA.58, OPE.60 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:E.154 CA.61: 7 residues within 4Å: Chain P: D.59, N.60, E.145, Q.146, D.147 Ligands: CA.62, OPE.64 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:D.59, P:E.145, P:E.145, P:Q.146, P:D.147 CA.62: 7 residues within 4Å: Chain P: E.145, D.147, E.154, E.157 Ligands: CA.61, CA.63, OPE.64 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:E.145, P:D.147, P:D.147, P:E.157 CA.63: 4 residues within 4Å: Chain P: E.154, E.157 Ligands: CA.62, OPE.64 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.154, P:E.154, P:E.157

16 x OPE: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER(Non-covalent)

OPE.4: 12 residues within 4Å: Chain A: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.1, CA.2, CA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.85, A:D.147, A:E.157 OPE.8: 12 residues within 4Å: Chain B: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.5, CA.6, CA.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.85, B:D.147, B:E.157 OPE.12: 12 residues within 4Å: Chain C: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.9, CA.10, CA.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.85, C:D.147, C:E.157 OPE.16: 12 residues within 4Å: Chain D: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.13, CA.14, CA.15 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.60, D:N.85, D:D.147, D:D.147, D:E.157 OPE.20: 12 residues within 4Å: Chain E: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.17, CA.18, CA.19 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.85, E:D.147, E:E.157 OPE.24: 12 residues within 4Å: Chain F: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.21, CA.22, CA.23 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.85, F:D.147, F:E.157 OPE.28: 12 residues within 4Å: Chain G: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.25, CA.26, CA.27 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:N.85, G:D.147, G:E.157 OPE.32: 12 residues within 4Å: Chain H: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.29, CA.30, CA.31 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:N.60, H:N.85, H:D.147, H:E.157 OPE.36: 12 residues within 4Å: Chain I: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.33, CA.34, CA.35 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:Y.49, I:N.60, I:N.85, I:D.147, I:E.157 OPE.40: 12 residues within 4Å: Chain J: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.37, CA.38, CA.39 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:Y.49, J:N.60, J:N.85, J:D.147, J:E.157 OPE.44: 12 residues within 4Å: Chain K: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.41, CA.42, CA.43 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:Y.49, K:N.60, K:N.85, K:D.147, K:E.157 OPE.48: 12 residues within 4Å: Chain L: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.45, CA.46, CA.47 5 PLIP interactions: 5 interactions with chain L Hydrogen bonds: L:Y.49, L:N.60, L:N.85, L:D.147, L:E.157 OPE.52: 12 residues within 4Å: Chain M: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.49, CA.50, CA.51 5 PLIP interactions: 5 interactions with chain M Hydrogen bonds: M:Y.49, M:N.60, M:N.85, M:D.147, M:E.157 OPE.56: 12 residues within 4Å: Chain N: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.53, CA.54, CA.55 5 PLIP interactions: 5 interactions with chain N Hydrogen bonds: N:Y.49, N:N.60, N:N.85, N:D.147, N:E.157 OPE.60: 12 residues within 4Å: Chain O: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.57, CA.58, CA.59 5 PLIP interactions: 5 interactions with chain O Hydrogen bonds: O:Y.49, O:N.60, O:N.85, O:D.147, O:E.157 OPE.64: 12 residues within 4Å: Chain P: Y.49, D.59, N.60, Q.79, N.85, E.145, D.147, E.154, E.157 Ligands: CA.61, CA.62, CA.63 5 PLIP interactions: 5 interactions with chain P Hydrogen bonds: P:Y.49, P:N.60, P:N.85, P:D.147, P: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: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

M
A

N
B

O
A

P
B

SAP-like pentraxin

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