SMTL ID : 4kgq.1

Crystal structure of a human light loop mutant in complex with dcr3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

hetero-6-6-mer

Ligands

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN.1: 10 residues within 4Å: Chain A: N.144, T.146 Chain B: P.25, Q.51, F.52, W.53, R.74, H.77, T.79, H.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.77, B:R.74, B:H.80, B:T.79 NAG-NAG-BMA-MAN.5: 10 residues within 4Å: Chain E: N.144, T.146 Chain F: P.25, Q.51, F.52, W.53, R.74, H.77, T.79, H.80 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.77, F:T.79, F:R.74, F:T.79 NAG-NAG-BMA-MAN.9: 10 residues within 4Å: Chain I: N.144, T.146 Chain J: P.25, Q.51, F.52, W.53, R.74, H.77, T.79, H.80 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:H.77, J:T.79, J:R.74, J:T.79

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 7 residues within 4Å: Chain A: P.25, Q.51, F.52, W.53 Chain B: N.144, T.146, A.147 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain E: P.25, Q.51, F.52, W.53 Chain F: N.144, T.146, A.147 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain I: P.25, Q.51, F.52, W.53 Chain J: N.144, T.146, A.147 No protein-ligand interaction detected (PLIP)

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: C.103, P.104, P.105, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.103, A:A.107, A:S.130, A:S.132, H2O.1 MG.4: 5 residues within 4Å: Chain B: C.103, P.104, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:P.104, B:A.107, B:S.130, B:S.132, H2O.2 MG.7: 6 residues within 4Å: Chain E: C.103, P.104, P.105, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:C.103, E:A.107, E:S.130, E:S.132, H2O.5 MG.8: 5 residues within 4Å: Chain F: C.103, P.104, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:P.104, F:A.107, F:S.130, F:S.132, H2O.7 MG.11: 6 residues within 4Å: Chain I: C.103, P.104, P.105, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:C.103, I:A.107, I:S.130, I:S.132, H2O.10 MG.12: 5 residues within 4Å: Chain J: C.103, P.104, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:P.104, J:A.107, J:S.130, J:S.132, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W. et al., Mechanistic basis for functional promiscuity in the TNF and TNF receptor superfamilies: structure of the LIGHT:DcR3 assembly. Structure (2014)

Release Date

2013-07-10

Peptides

Tumor necrosis factor receptor superfamily member 6B: ABEFIJ
Tumor necrosis factor ligand superfamily member 14: CDGHKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

E
C

F
D

I
C

J
D

C
A

D
B

G
A

H
B

K
A

L
B

Tumor necrosis factor receptor superfamily member 6B

Tumor necrosis factor ligand superfamily member 14

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