SMTL ID : 7cpd.1

Crystal structure of T2R-TTL-(+)-6-Br-JP18 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 28 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, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.2 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.98, A:A.99, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:E.183, A:N.206, A:N.206, A:Y.224, A:Y.224, A:N.228, A:N.228 Water bridges: A:D.98, A:F.141 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.10: 27 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.11 27 PLIP interactions: 27 interactions with chain C Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:Q.15, C:D.98, C:A.99, C:N.101, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:E.183, C:N.206, C:N.206, C:Y.224, C:Y.224, C:N.228, C:N.228 Water bridges: C:G.10, C:G.13, C:D.98, C:D.98, C:D.98 pi-Stacking: C:Y.224, C:Y.224

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

MG.2: 1 residues within 4Å: Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: Q.11, N.99, D.177 Ligands: GDP.7 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: Q.11, D.69, E.71 Ligands: GTP.10 No protein-ligand interaction detected (PLIP)

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

CA.3: 4 residues within 4Å: Chain A: D.39, T.41, G.44, 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.6: 2 residues within 4Å: Chain B: E.108, E.111 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.111 CA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x G9U: (6R)-6-[(6-bromanyl-1H-indol-3-yl)methyl]-6,7,8,9-tetrahydrobenzo[7]annulen-5-one(Non-covalent)

G9U.4: 20 residues within 4Å: Chain A: T.179, A.180, V.181 Chain B: V.236, T.237, C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, V.313, A.314, I.316, N.348, K.350, A.352 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.240, B:L.246, B:A.248, B:L.253, B:N.256, B:A.352 Hydrogen bonds: B:D.249, B:K.350, A:T.179 Halogen bonds: B:N.348 G9U.13: 21 residues within 4Å: Chain C: N.101, T.179, A.180, V.181 Chain D: V.236, C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, V.313, A.314, N.348, V.349, K.350, A.352, I.368 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.240, D:L.246, D:A.248, D:L.253, D:L.253, D:L.253, D:N.256, D:I.368, C:V.181 Hydrogen bonds: D:D.249, C:T.179

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

GDP.7: 23 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, L.207, Y.222, L.225, N.226 Ligands: MG.5 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:Q.15, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:T.143, B:G.144, B:D.177, B:E.181, B:N.204, B:N.204, B:Y.222, B:Y.222, B:N.226, B:N.226 Water bridges: B:A.97, B:S.138, B:G.140, B:G.140, B:S.145, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.14: 22 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:N.204, D:N.204 Water bridges: D:S.138, D:G.140, D:N.204

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

MES.8: 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: 5 interactions with chain B Hydrogen bonds: B:P.160, B:D.161 Water bridges: B:R.156 Salt bridges: B:D.197, B:R.251

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain C: S.287, V.288, A.289, D.322, D.327, R.373 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.288, C:A.289, C:D.327, C:R.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, H. et al., Crystal structure of T2R-TTL-(+)-6-Br-JP18 complex. To Be Published

Release Date

2021-08-11

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta-2B 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-2B chain

Stathmin-4

Tubulin tyrosine ligase

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