SMTL ID : 7emj.1

Crystal structure of T2R-TTL-Barbigerone complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

3 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 30 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, A.174, V.177, S.178, E.183, N.206, I.209, Y.224, L.227, N.228, I.231 Chain B: K.252 Ligands: MG.2 26 PLIP interactions: 23 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:G.13, A:N.101, A:G.142, A:G.142, A:A.174, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.11: 30 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, A.174, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain D: K.252 Ligands: MG.12 25 PLIP interactions: 23 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:Q.15, C:A.99, C:A.100, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:N.206, C:N.206, C:Y.224, C:Y.224, C:N.228, C:N.228 Water bridges: C:S.140, C:F.141, C:G.142, C:T.179, D:K.252 pi-Stacking: C:Y.224 Salt bridges: D:K.252 GTP.14: 29 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, A.97, G.98, N.99, N.100, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, P.171, S.172, V.175, S.176, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.15 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:Q.15, D:A.97, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:G.144, D:S.176, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:Q.11, D:G.13, D:S.138, D:L.139, D:G.140, D:S.145, D:S.172

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain A: Q.11 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.10 No protein-ligand interaction detected (PLIP) MG.12: 6 residues within 4Å: Chain C: Q.11, D.69, E.71, D.98 Chain D: K.252 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain D: Q.11 Ligands: GTP.14 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain F: K.74, E.331, N.333 Ligands: ACP.17 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.331, F:E.331

6 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 8 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, D.47, F.49, N.50, E.55 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.39, A:D.39, A:T.41, A:G.44, A:E.55 CA.4: 2 residues within 4Å: Chain A: S.158, K.166 No protein-ligand interaction detected (PLIP) CA.7: 1 residues within 4Å: Chain B: D.114 No protein-ligand interaction detected (PLIP) CA.8: 1 residues within 4Å: Chain B: E.111 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.111, B:E.111 CA.13: 6 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, F.49, E.55 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.39, C:T.41, C:T.41, C:G.44, C:E.55 CA.16: 5 residues within 4Å: Chain D: F.294, R.306, Y.310, N.337, Y.340 No protein-ligand interaction detected (PLIP)

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 12 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, M.164, E.194, N.195, T.196, D.197, R.251 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:R.105, B:R.156, B:R.251 Salt bridges: B:D.197, B:R.251

1 x J6L: 8,8-dimethyl-3-(2,4,5-trimethoxyphenyl)pyrano[2,3-f]chromen-4-one(Non-covalent)

J6L.9: 24 residues within 4Å: Chain A: T.179 Chain B: I.4, Y.50, Q.134, N.165, T.166, F.167, E.198, Y.200, V.236, T.237, C.239, L.240, L.250, L.253, M.257, F.266, A.314, A.315, V.316, K.350, T.351, A.352, I.368 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.250, B:L.253, B:A.314, B:V.316, B:A.352, B:I.368, A:T.179 Hydrogen bonds: B:N.165

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.10: 27 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, A.97, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, P.171, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.5 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.141, B:G.142, B:T.143, B:T.143, B:G.144, B:D.177, B:D.177, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 Water bridges: B:Q.11, B:S.138, B:S.138, B:G.140, B:T.143, B:T.143, B:S.145

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.17: 23 residues within 4Å: Chain F: K.74, P.95, I.148, K.150, I.160, Q.183, K.184, Y.185, L.186, K.198, D.200, R.202, R.222, H.239, L.240, T.241, N.242, D.318, M.320, I.330, E.331, N.333 Ligands: MG.18 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:K.74, F:Q.183, F:Q.183, F:L.186, F:K.198, F:D.200, F:D.200, F:R.202, F:R.222, F:R.222, F:T.241, F:N.242, F:D.318, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J.H. et al., Crystal structure of T2R-TTL-barbigerone complex. To Be Published

Release Date

2022-04-20

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta chain: BD
Stathmin-4: E
Tubulin tyrosine ligase: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

Tubulin alpha-1B chain

Tubulin beta chain

Stathmin-4

Tubulin tyrosine ligase

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