SMTL ID : 9c6r.1

Blood cell-specific tubulin in complex with Cryptophycin-52

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-8-mer

Ligands

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

GTP.1: 20 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, D.69, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.11, A:Q.11, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:V.177, A:T.179, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 pi-Cation interactions: A:Y.224 Salt bridges: D:K.252 GTP.4: 21 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, D.69, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, V.177, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.11, C:Q.11, C:A.99, C:A.100, C:N.101, C:N.101, C:S.140, C:G.144, C:T.145, C:G.146, C:V.177, C:T.179, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 pi-Cation interactions: C:Y.224 Salt bridges: F:K.252 GTP.7: 20 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, D.69, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 21 PLIP interactions: 20 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:Q.11, E:Q.11, E:A.99, E:A.100, E:N.101, E:N.101, E:S.140, E:G.144, E:T.145, E:G.146, E:V.177, E:T.179, E:E.183, E:N.206, E:N.206, E:N.228, E:N.228 pi-Stacking: E:Y.224, E:Y.224 pi-Cation interactions: E:Y.224 Salt bridges: H:K.252 GTP.11: 21 residues within 4Å: Chain G: G.10, Q.11, A.12, Q.15, D.69, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, V.177, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 21 PLIP interactions: 20 interactions with chain G, 1 interactions with chain J Hydrogen bonds: G:Q.11, G:Q.11, G:A.99, G:A.100, G:N.101, G:N.101, G:S.140, G:G.144, G:T.145, G:G.146, G:V.177, G:T.179, G:E.183, G:N.206, G:N.206, G:N.228, G:N.228 pi-Stacking: G:Y.224, G:Y.224 pi-Cation interactions: G:Y.224 Salt bridges: J:K.252 GTP.13: 20 residues within 4Å: Chain I: G.10, Q.11, A.12, Q.15, D.69, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 21 PLIP interactions: 20 interactions with chain I, 1 interactions with chain L Hydrogen bonds: I:Q.11, I:Q.11, I:A.99, I:A.100, I:N.101, I:N.101, I:S.140, I:G.144, I:T.145, I:G.146, I:V.177, I:T.179, I:E.183, I:N.206, I:N.206, I:N.228, I:N.228 pi-Stacking: I:Y.224, I:Y.224 pi-Cation interactions: I:Y.224 Salt bridges: L:K.252 GTP.16: 21 residues within 4Å: Chain K: G.10, Q.11, A.12, Q.15, D.69, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, V.177, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 21 PLIP interactions: 20 interactions with chain K, 1 interactions with chain N Hydrogen bonds: K:Q.11, K:Q.11, K:A.99, K:A.100, K:N.101, K:N.101, K:S.140, K:G.144, K:T.145, K:G.146, K:V.177, K:T.179, K:E.183, K:N.206, K:N.206, K:N.228, K:N.228 pi-Stacking: K:Y.224, K:Y.224 pi-Cation interactions: K:Y.224 Salt bridges: N:K.252 GTP.19: 20 residues within 4Å: Chain M: G.10, Q.11, A.12, Q.15, D.69, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 21 PLIP interactions: 20 interactions with chain M, 1 interactions with chain P Hydrogen bonds: M:Q.11, M:Q.11, M:A.99, M:A.100, M:N.101, M:N.101, M:S.140, M:G.144, M:T.145, M:G.146, M:V.177, M:T.179, M:E.183, M:N.206, M:N.206, M:N.228, M:N.228 pi-Stacking: M:Y.224, M:Y.224 pi-Cation interactions: M:Y.224 Salt bridges: P:K.252 GTP.22: 21 residues within 4Å: Chain O: G.10, Q.11, A.12, Q.15, D.69, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, V.177, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 21 PLIP interactions: 20 interactions with chain O, 1 interactions with chain B Hydrogen bonds: O:Q.11, O:Q.11, O:A.99, O:A.100, O:N.101, O:N.101, O:S.140, O:G.144, O:T.145, O:G.146, O:V.177, O:T.179, O:E.183, O:N.206, O:N.206, O:N.228, O:N.228 pi-Stacking: O:Y.224, O:Y.224 pi-Cation interactions: O:Y.224 Salt bridges: B:K.252

8 x YGY: Cryptophycin 52(Non-covalent)

YGY.2: 19 residues within 4Å: Chain A: T.257, N.258, L.259, V.260, P.261, M.313, V.344, W.346, C.347, T.349, K.352 Chain B: G.98, N.99, N.100, K.103, V.179, V.180, F.394, W.397 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:T.257, B:K.103, B:V.179, B:V.180, B:V.180, B:F.394, B:F.394, B:F.394, B:W.397 Hydrogen bonds: A:T.349, B:N.99 YGY.5: 22 residues within 4Å: Chain C: T.253, T.257, N.258, L.259, V.260, P.261, M.313, V.344, W.346, C.347, T.349, K.352 Chain D: A.97, G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:K.103, D:V.179, D:V.180, D:V.180, D:F.394, D:F.394, D:F.394, D:W.397, D:W.397, C:T.253 Hydrogen bonds: D:N.99, C:T.349 YGY.8: 20 residues within 4Å: Chain E: T.257, N.258, L.259, V.260, P.261, M.313, V.344, W.346, C.347, T.349, K.352 Chain F: G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:K.103, F:V.179, F:F.394, F:F.394, F:F.394, F:W.397, E:T.257 Hydrogen bonds: F:N.99, E:T.349 YGY.10: 22 residues within 4Å: Chain G: T.253, T.257, N.258, L.259, V.260, P.261, M.313, V.344, W.346, C.347, T.349, K.352 Chain H: A.97, G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:K.103, H:V.179, H:V.180, H:V.180, H:F.394, H:F.394, H:F.394, H:W.397, H:W.397, G:T.253 Hydrogen bonds: H:N.99, G:T.349 YGY.14: 20 residues within 4Å: Chain I: T.257, N.258, L.259, V.260, P.261, M.313, V.344, W.346, C.347, T.349, K.352 Chain J: G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 9 PLIP interactions: 7 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:K.103, J:V.179, J:F.394, J:F.394, J:F.394, J:W.397, I:T.257 Hydrogen bonds: J:N.99, I:T.349 YGY.17: 22 residues within 4Å: Chain K: T.253, T.257, N.258, L.259, V.260, P.261, M.313, V.344, W.346, C.347, T.349, K.352 Chain L: A.97, G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 12 PLIP interactions: 10 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:K.103, L:V.179, L:V.180, L:V.180, L:F.394, L:F.394, L:F.394, L:W.397, L:W.397, K:T.253 Hydrogen bonds: L:N.99, K:T.349 YGY.20: 20 residues within 4Å: Chain M: T.257, N.258, L.259, V.260, P.261, M.313, V.344, W.346, C.347, T.349, K.352 Chain N: G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 9 PLIP interactions: 7 interactions with chain N, 2 interactions with chain M Hydrophobic interactions: N:K.103, N:V.179, N:F.394, N:F.394, N:F.394, N:W.397, M:T.257 Hydrogen bonds: N:N.99, M:T.349 YGY.23: 22 residues within 4Å: Chain O: T.253, T.257, N.258, L.259, V.260, P.261, M.313, V.344, W.346, C.347, T.349, K.352 Chain P: A.97, G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 12 PLIP interactions: 10 interactions with chain P, 2 interactions with chain O Hydrophobic interactions: P:K.103, P:V.179, P:V.180, P:V.180, P:F.394, P:F.394, P:F.394, P:W.397, P:W.397, O:T.253 Hydrogen bonds: P:N.99, O:T.349

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

GDP.3: 18 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, V.175, S.176, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:A.97, B:G.98, B:N.99, B:S.138, B:G.141, B:G.142, B:T.143, B:S.176, B:S.176, B:N.204, B:N.204, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 GDP.6: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, V.175, S.176, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:A.97, D:G.98, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:S.176, D:S.176, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222 GDP.9: 18 residues within 4Å: Chain F: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, V.175, S.176, E.181, N.204, Y.222, N.226 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:Q.11, F:C.12, F:G.98, F:N.99, F:S.138, F:G.141, F:G.142, F:T.143, F:S.176, F:S.176, F:N.204, F:N.204, F:N.226, F:N.226 pi-Stacking: F:Y.222, F:Y.222 GDP.12: 18 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, V.175, S.176, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:C.12, H:A.97, H:G.98, H:N.99, H:S.138, H:G.141, H:G.142, H:T.143, H:S.176, H:S.176, H:N.204, H:N.204, H:N.226, H:N.226 pi-Stacking: H:Y.222, H:Y.222 GDP.15: 18 residues within 4Å: Chain J: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, V.175, S.176, E.181, N.204, Y.222, N.226 16 PLIP interactions: 16 interactions with chain J Hydrogen bonds: J:Q.11, J:C.12, J:G.98, J:N.99, J:S.138, J:G.141, J:G.142, J:T.143, J:S.176, J:S.176, J:N.204, J:N.204, J:N.226, J:N.226 pi-Stacking: J:Y.222, J:Y.222 GDP.18: 18 residues within 4Å: Chain L: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, V.175, S.176, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain L Hydrogen bonds: L:Q.11, L:Q.11, L:C.12, L:A.97, L:G.98, L:N.99, L:S.138, L:G.141, L:G.142, L:T.143, L:S.176, L:S.176, L:N.204, L:N.204, L:N.226, L:N.226 pi-Stacking: L:Y.222, L:Y.222 GDP.21: 18 residues within 4Å: Chain N: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, V.175, S.176, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain N Hydrogen bonds: N:Q.11, N:C.12, N:A.97, N:G.98, N:N.99, N:S.138, N:G.141, N:G.142, N:T.143, N:S.176, N:S.176, N:N.204, N:N.204, N:N.226, N:N.226 pi-Stacking: N:Y.222, N:Y.222 GDP.24: 18 residues within 4Å: Chain P: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, V.175, S.176, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain P Hydrogen bonds: P:Q.11, P:Q.11, P:C.12, P:A.97, P:G.98, P:N.99, P:S.138, P:G.141, P:G.142, P:T.143, P:S.176, P:S.176, P:N.204, P:N.204, P:N.226, P:N.226 pi-Stacking: P:Y.222, P:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Montecinos, F. et al., Structure of blood cell-specific tubulin and demonstration of dimer spacing compaction in a single protofilament. J.Biol.Chem. (2024)

Release Date

2025-01-01

Peptides

Detyrosinated tubulin alpha-1A chain: ACEGIKMO
Tubulin beta-6 chain: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
F

E
K

G
P

I
U

K
Z

M
e

O
j

B
B

D
G

F
L

H
Q

J
V

L
a

N
f

P
k

Detyrosinated tubulin alpha-1A chain

Tubulin beta-6 chain

Related Entries With Identical Sequence