SMTL ID : 8r67.1

tubulin-cryptophycin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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 29 PLIP interactions: 25 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:F.141, A:T.145, A:A.174, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.12: 25 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, S.178, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.13 27 PLIP interactions: 23 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:D.69, 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:F.141, C:T.145, C:T.145, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.71 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain C: D.69, E.71 Ligands: GTP.12 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain D: Q.11 Ligands: GDP.16 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain F: K.74, E.331, N.333 Ligands: ACP.23 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, E.55 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:D.39, A:G.44, A:E.55, H2O.2 CA.4: 1 residues within 4Å: Chain E: D.42 No protein-ligand interaction detected (PLIP) CA.11: 2 residues within 4Å: Chain B: E.108, E.111 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.111, H2O.6 CA.14: 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:E.55, C:E.55, H2O.9

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

GDP.5: 19 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, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 Ligands: MG.6 23 PLIP interactions: 23 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:V.175, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:G.13, B:N.99, B:G.140, B:G.140, B:G.141, B:G.141, B:T.143, B:D.177 pi-Stacking: B:Y.222, B:Y.222 GDP.16: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.17 12 PLIP interactions: 12 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

5 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 7 residues within 4Å: Chain B: A.18, K.19, E.22, S.75, V.76, G.79, P.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.75 IMD.8: 7 residues within 4Å: Chain B: A.206, D.209, I.210, R.213, S.296, K.297, M.299 No protein-ligand interaction detected (PLIP) IMD.15: 1 residues within 4Å: Chain C: D.431 1 PLIP interactions: 1 interactions with chain C pi-Stacking: C:Y.262 IMD.20: 2 residues within 4Å: Chain E: E.56, R.59 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.56, E:R.59 pi-Cation interactions: E:R.59 IMD.21: 3 residues within 4Å: Chain E: E.57, R.58, Y.61 No protein-ligand interaction detected (PLIP)

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

MES.9: 11 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, M.164, E.194, N.195, T.196, D.197, R.251 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.156, B:R.156, B:R.251, B:R.251 Salt bridges: B:D.197, B:R.251

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain B: V.175, P.220, T.221, Y.222 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.222

2 x Y74: 2-[(3~{S},10~{R},13~{E},16~{S})-10-[(3-chloranyl-4-methoxy-phenyl)methyl]-6,6-dimethyl-2,5,9,12-tetrakis(oxidanylidene)-16-[(1~{S})-1-[(2~{R},3~{R})-3-phenyloxiran-2-yl]ethyl]-1,4-dioxa-8,11-diazacyclohexadec-13-en-3-yl]ethanoic acid(Non-covalent)

Y74.18: 10 residues within 4Å: Chain D: P.171, S.172, P.173, V.175, S.176, D.177, T.178, E.181, P.182, Q.384 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:P.171, D:P.173, D:D.177, D:E.181, D:P.182 Hydrogen bonds: D:P.173, D:S.176 Y74.19: 11 residues within 4Å: Chain D: A.97, G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397, Y.398 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:K.103, D:V.179, D:V.180, D:V.180, D:F.394, D:W.397, D:W.397 Hydrogen bonds: D:N.99, D:N.100, D:V.179

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

ACP.23: 21 residues within 4Å: Chain F: K.74, 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, I.330, E.331, N.333 Ligands: MG.22 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, F:Q.183, F:L.186, F:K.198, F:R.202, F:T.241, F:T.241, F:N.242, F:D.318, F:E.331, F:N.333, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abel, A.C. et al., Bridging the maytansine and vinca sites: Cryptophycins target beta-tubulin's T5-loop. J.Biol.Chem. (2024)

Release Date

2024-05-22

Peptides

Detyrosinated 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

Detyrosinated tubulin alpha-1B chain

Tubulin beta-2B chain

Stathmin-4

Tubulin tyrosine ligase

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