SMTL ID : 9bn7.1

X-ray crystal structure of TNFa-VNAR C4 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-3-3-mer

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: K.65, Y.115, D.143, A.145, E.146, Q.149 Chain B: I.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.65, A:E.146, A:Q.149 EDO.6: 7 residues within 4Å: Chain A: I.97 Chain C: K.65, Y.115, D.143, A.145, E.146, Q.149 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.65, C:E.146, C:Q.149 EDO.8: 6 residues within 4Å: Chain D: A.1, S.27, C.29, W.87, S.95, V.99 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.28, D:S.95 EDO.11: 4 residues within 4Å: Chain E: Y.37, E.46, K.84, Y.100 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.46, E:K.84, E:Y.100

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 9 residues within 4Å: Chain A: K.98, P.117, Y.119 Chain B: K.98, P.117, I.118, Y.119 Chain C: K.98 Ligands: SO4.7 8 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:P.117, B:Y.119, A:Y.119 Salt bridges: B:K.98, A:K.98, C:K.98 Water bridges: A:K.98, A:K.98 SO4.3: 7 residues within 4Å: Chain B: K.65, Y.115, D.143, A.145, E.146, Q.149 Chain C: I.97 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.115, B:E.146, B:Q.149 Salt bridges: B:K.65 SO4.4: 9 residues within 4Å: Chain A: L.57, Y.119, G.121 Chain B: L.57, Y.119, G.121 Chain C: L.57, Y.119, G.121 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.119, A:Y.119 SO4.5: 6 residues within 4Å: Chain A: K.11, L.157 Chain B: K.11, L.157 Chain C: K.11, L.157 8 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: C:L.157, B:L.157, B:L.157, A:L.157, A:L.157 Salt bridges: C:K.11, B:K.11, A:K.11 SO4.7: 7 residues within 4Å: Chain A: K.98, E.116 Chain B: K.98, E.116 Chain C: K.98, E.116 Ligands: SO4.2 9 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, 3 interactions with chain C Water bridges: A:E.116, A:E.116, A:E.116, A:E.116, C:E.116 Salt bridges: A:K.98, B:K.98, C:K.98 Hydrogen bonds: C:E.116 SO4.9: 2 residues within 4Å: Chain D: R.25, D.26 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.26

4 x NI: NICKEL (II) ION(Non-covalent)

NI.10: 3 residues within 4Å: Chain D: T.14, H.110, H.111 No protein-ligand interaction detected (PLIP) NI.12: 3 residues within 4Å: Chain E: T.14, H.110, H.111 No protein-ligand interaction detected (PLIP) NI.13: 2 residues within 4Å: Chain F: E.13, H.111 No protein-ligand interaction detected (PLIP) NI.14: 3 residues within 4Å: Chain F: T.14, H.110, H.111 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ubah, O.C. et al., X-ray crystal structure of TNFa VNAR complex. To Be Published

Release Date

2025-11-05

Peptides

Tumor necrosis factor: ABC
VNARC4: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Tumor necrosis factor

VNARC4

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