SMTL ID : 5hch.1

X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: CA.2, 61J.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.95, A:D.99, A:D.101, A:D.104, A:D.104 CA.2: 7 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Chain J: G.114 Ligands: CA.1, 61J.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain J Metal complexes: A:N.21, A:D.101, A:D.104, J:G.114 CA.5: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: CA.6, 61J.8 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.95, D:D.99, D:D.101, D:D.104, D:D.104 CA.6: 7 residues within 4Å: Chain D: N.21, D.101, N.103, D.104 Chain G: G.114 Ligands: CA.5, 61J.8 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain G Metal complexes: D:N.21, D:D.101, D:D.104, G:G.114 CA.9: 6 residues within 4Å: Chain G: E.95, D.99, D.101, D.104 Ligands: CA.10, 61J.12 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.95, G:D.99, G:D.101, G:D.104, G:D.104 CA.10: 7 residues within 4Å: Chain D: G.114 Chain G: N.21, D.101, N.103, D.104 Ligands: CA.9, 61J.12 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain D Metal complexes: G:N.21, G:D.101, G:D.104, D:G.114 CA.13: 6 residues within 4Å: Chain J: E.95, D.99, D.101, D.104 Ligands: CA.14, 61J.16 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.95, J:D.99, J:D.101, J:D.104, J:D.104 CA.14: 7 residues within 4Å: Chain A: G.114 Chain J: N.21, D.101, N.103, D.104 Ligands: CA.13, 61J.16 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain A Metal complexes: J:N.21, J:D.101, J:D.104, A:G.114

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x 61J: (6S)-2,6-anhydro-1-deoxy-6-(2-{[(S)-hydroxy(oxido)-lambda~5~-phosphanyl]oxy}ethyl)-D-galactitol(Non-covalent)

61J.4: 14 residues within 4Å: Chain A: N.21, S.22, S.23, E.95, D.96, G.97, D.99, D.101, D.104 Chain B: C.13 Chain C: G.1 Chain J: G.114 Ligands: CA.1, CA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.23, A:G.97, A:D.104 61J.8: 14 residues within 4Å: Chain D: N.21, S.22, S.23, E.95, D.96, G.97, D.99, D.101, D.104 Chain E: C.13 Chain F: G.1 Chain G: G.114 Ligands: CA.5, CA.6 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.23, D:G.97, D:D.104 61J.12: 14 residues within 4Å: Chain D: G.114 Chain G: N.21, S.22, S.23, E.95, D.96, G.97, D.99, D.101, D.104 Chain H: C.13 Chain I: G.1 Ligands: CA.9, CA.10 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.23, G:G.97, G:D.104 61J.16: 14 residues within 4Å: Chain A: G.114 Chain J: N.21, S.22, S.23, E.95, D.96, G.97, D.99, D.101, D.104 Chain K: C.13 Chain L: G.1 Ligands: CA.13, CA.14 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain J Hydrogen bonds: A:G.114, J:S.23, J:E.95, J:G.97, J:D.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roethlisberger, P. et al., X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair. Chem.Commun.(Camb.) (2016)

Release Date

2016-03-02

Peptides

Fucose-binding lectin: ADGJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

Fucose-binding lectin

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