SMTL ID : 6i5c.1

Long wavelength native-SAD phasing of Tubulin-Stathmin-TTL complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 25 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, D.69, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, V.177, S.178, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 32 PLIP interactions: 28 interactions with chain A, 4 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:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:G.13, A:E.71, A:D.98, A:F.141, A:T.145, A:T.145, A:A.174, A:E.183, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.10: 24 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, D.69, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.11 31 PLIP interactions: 26 interactions with chain C, 5 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:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:G.13, C:E.71, C:N.101, C:F.141, C:T.145, C:T.145, C:E.183, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.69 Chain B: K.252 Ligands: GTP.1 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) MG.16: 6 residues within 4Å: Chain F: R.202, R.222, D.318, E.331, N.333 Ligands: ACP.17 No protein-ligand interaction detected (PLIP)

5 x CA: CALCIUM ION(Non-covalent)

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: 1 residues within 4Å: Chain B: E.111 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain B: Q.11 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) CA.12: 4 residues within 4Å: Chain C: D.39, T.41, G.44, E.55 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, C:T.41, C:G.44, C:E.55, H2O.8 CA.15: 3 residues within 4Å: Chain D: Q.11, N.99 Ligands: GDP.14 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: Y.161, G.162, K.163, K.164 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain C: Q.233, V.362, V.363, L.368 Ligand excluded by PLIP

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

GDP.5: 22 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, 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: CA.9 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:D.177, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:G.13, B:G.98, B:G.140, B:G.141, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.14: 23 residues within 4Å: Chain D: 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, S.176, E.181, N.204, L.207, Y.222, L.225, N.226 Ligands: CA.15 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:S.138, D:G.140, D:G.141, D:T.143, D:S.145, D:S.176, D:Y.222 pi-Stacking: D:Y.222, D:Y.222

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

MES.7: 9 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, M.164, N.195, D.197, R.251 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:R.156, B:R.251, A:R.105 Salt bridges: B:D.197, B:R.251 MES.8: 8 residues within 4Å: Chain B: F.294, D.295, S.296, D.304, P.305, R.306, N.337, Y.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.296, B:R.306 Salt bridges: B:R.306

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

ACP.17: 18 residues within 4Å: Chain F: K.74, I.148, K.150, Q.183, K.184, Y.185, L.186, K.198, D.200, H.239, L.240, T.241, N.242, M.320, I.330, E.331, N.333 Ligands: MG.16 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, F:Q.183, F:L.186, F:K.198, F:D.200, F:D.200, F:T.241, F:T.241, F:N.242, F:E.331, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basu, S. et al., Long-wavelength native-SAD phasing: opportunities and challenges. Iucrj (2019)

Release Date

2019-03-13

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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