SMTL ID : 4ihj.1

Crystal structure of tubulin-stathmin-TTL-ADP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 31 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, L.70, 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 B: K.252 Ligands: MG.2 29 PLIP interactions: 23 interactions with chain A, 6 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.143, 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:L.70, A:N.101, A:F.141, B:K.252, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.11: 32 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, L.70, D.98, A.99, A.100, N.101, N.102, 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 28 PLIP interactions: 24 interactions with chain C, 4 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:N.228, C:N.228 Water bridges: C:G.13, C:N.101, C:N.101, C:F.141, C:V.177, 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

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: Q.11, D.69, E.71, D.98 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.6 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: GDP.14 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain D: N.99 Ligands: GDP.14 No protein-ligand interaction detected (PLIP) MG.17: 6 residues within 4Å: Chain F: R.222, N.242, D.318, E.331, N.333 Ligands: ADP.19 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.318, F:E.331, H2O.9, H2O.40 MG.18: 5 residues within 4Å: Chain A: E.450 Chain F: K.74, E.331, N.333 Ligands: ADP.19 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.331, F:E.331, H2O.40

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, F.49, E.55 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:T.41, A:G.44, A:E.55, H2O.4 CA.5: 4 residues within 4Å: Chain A: S.158, K.166, H.197 Chain E: D.42 No protein-ligand interaction detected (PLIP) CA.8: 1 residues within 4Å: Chain B: E.111 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.111, H2O.12, H2O.13, H2O.13 CA.13: 7 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, F.49, E.55, H.61 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, C:T.41, C:E.55, C:E.55, H2O.23

1 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

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

GDP.6: 28 residues within 4Å: Chain B: G.10, Q.11, C.12, G.13, Q.15, I.16, A.97, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, P.171, S.172, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.7 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:Q.15, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:V.175, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:A.97, B:S.138, B:L.139, B:G.141, B:T.143, B:T.143, B:S.145, B:V.175, B:E.181 pi-Stacking: B:Y.222, B:Y.222 GDP.14: 26 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, A.97, S.138, G.140, G.141, G.142, T.143, G.144, 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, MG.16 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:Q.15, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:G.144, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:S.138, D:L.139, D:S.145, D:S.145 pi-Stacking: D:Y.222, D:Y.222

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

MES.9: 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 Water bridges: B:R.156, B:P.160, B:R.251 Salt bridges: B:D.197, B:R.251 MES.10: 11 residues within 4Å: Chain B: F.294, D.295, S.296, K.297, P.305, R.306, Y.310, V.333, N.337, Y.340, F.341 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.294, B:S.296 Water bridges: B:S.296 Salt bridges: B:R.306

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.19: 20 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, H.239, L.240, T.241, N.242, M.320, I.330, E.331 Ligands: MG.17, MG.18 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: 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 Water bridges: F:N.333, F:N.333 Salt bridges: F:K.74, F:K.74, F:K.150

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 8 residues within 4Å: Chain F: Y.211, I.213, R.292, M.296, L.378, H.379, H.380, H.381 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.292, F:H.380, F:H.380, F:H.381 Water bridges: F:I.213, F:L.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prota, A.E. et al., Structural basis of tubulin tyrosination by tubulin tyrosine ligase. J.Cell Biol. (2013)

Release Date

2013-02-13

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta-2B chain: BD
Stathmin-4: E
TUBULIN TYROSINE LIGASE, TTL: 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, TTL

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