SMTL ID : 9c6s.1

18-mer blood cell-specific tubulin in complex with Cryptophycin-52

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-9-9-mer

Ligands

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

GTP.1: 19 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, D.69, N.101, S.140, G.142, G.143, G.144, T.145, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain R: K.252 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain R Hydrogen bonds: A:Q.11, A:A.12, A:S.140, A:S.140, A:G.143, A:G.144, A:T.145, A:T.145, A:V.177, A:E.183, A:N.206, A:N.206, A:N.228 pi-Stacking: A:Y.224, A:Y.224 pi-Cation interactions: A:Y.224 Salt bridges: R:K.252, R:K.252 GTP.4: 19 residues within 4Å: Chain B: K.252 Chain C: G.10, Q.11, A.12, Q.15, D.69, N.101, S.140, G.143, G.144, T.145, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.11, C:A.12, C:N.101, C:S.140, C:S.140, C:G.143, C:G.144, C:T.145, C:T.145, C:V.177, C:E.183, C:N.206, C:N.206, C:N.228 pi-Stacking: C:Y.224, C:Y.224 pi-Cation interactions: C:Y.224 Salt bridges: B:K.252, B:K.252 GTP.7: 20 residues within 4Å: Chain D: K.252 Chain E: G.10, Q.11, A.12, Q.15, D.69, N.101, S.140, G.142, G.143, G.144, T.145, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 19 PLIP interactions: 17 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:Q.11, E:A.12, E:N.101, E:S.140, E:S.140, E:G.143, E:G.144, E:T.145, E:T.145, E:V.177, E:E.183, E:N.206, E:N.206, E:N.228 pi-Stacking: E:Y.224, E:Y.224 pi-Cation interactions: E:Y.224 Salt bridges: D:K.252, D:K.252 GTP.10: 20 residues within 4Å: Chain F: K.252 Chain G: G.10, Q.11, A.12, Q.15, D.69, N.101, S.140, G.142, G.143, G.144, T.145, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 18 PLIP interactions: 16 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:Q.11, G:A.12, G:S.140, G:S.140, G:G.143, G:G.144, G:T.145, G:T.145, G:V.177, G:E.183, G:N.206, G:N.206, G:N.228 pi-Stacking: G:Y.224, G:Y.224 pi-Cation interactions: G:Y.224 Salt bridges: F:K.252, F:K.252 GTP.13: 20 residues within 4Å: Chain H: K.252 Chain I: G.10, Q.11, A.12, Q.15, D.69, N.101, S.140, G.142, G.143, G.144, T.145, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 20 PLIP interactions: 18 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:Q.11, I:A.12, I:N.101, I:S.140, I:S.140, I:G.143, I:G.144, I:T.145, I:T.145, I:V.177, 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: H:K.252, H:K.252 GTP.16: 20 residues within 4Å: Chain J: K.252 Chain K: G.10, Q.11, A.12, Q.15, D.69, N.101, S.140, G.142, G.143, G.144, T.145, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 18 PLIP interactions: 16 interactions with chain K, 2 interactions with chain J Hydrogen bonds: K:Q.11, K:A.12, K:S.140, K:S.140, K:G.143, K:G.144, K:T.145, K:T.145, K:V.177, K:E.183, K:N.206, K:N.206, K:N.228 pi-Stacking: K:Y.224, K:Y.224 pi-Cation interactions: K:Y.224 Salt bridges: J:K.252, J:K.252 GTP.19: 20 residues within 4Å: Chain L: K.252 Chain M: G.10, Q.11, A.12, Q.15, D.69, N.101, S.140, G.142, G.143, G.144, T.145, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 18 PLIP interactions: 16 interactions with chain M, 2 interactions with chain L Hydrogen bonds: M:Q.11, M:A.12, M:S.140, M:S.140, M:G.143, M:G.144, M:T.145, M:T.145, M:V.177, M:E.183, M:N.206, M:N.206, M:N.228 pi-Stacking: M:Y.224, M:Y.224 pi-Cation interactions: M:Y.224 Salt bridges: L:K.252, L:K.252 GTP.22: 20 residues within 4Å: Chain N: K.252 Chain O: G.10, Q.11, A.12, Q.15, D.69, N.101, S.140, G.142, G.143, G.144, T.145, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 19 PLIP interactions: 2 interactions with chain N, 17 interactions with chain O Salt bridges: N:K.252, N:K.252 Hydrogen bonds: O:Q.11, O:A.12, O:N.101, O:S.140, O:S.140, O:G.143, O:G.144, O:T.145, O:T.145, O:V.177, O:E.183, O:N.206, O:N.206, O:N.228 pi-Stacking: O:Y.224, O:Y.224 pi-Cation interactions: O:Y.224 GTP.25: 20 residues within 4Å: Chain P: K.252 Chain Q: G.10, Q.11, A.12, Q.15, D.69, N.101, S.140, G.142, G.143, G.144, T.145, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 18 PLIP interactions: 16 interactions with chain Q, 2 interactions with chain P Hydrogen bonds: Q:Q.11, Q:A.12, Q:S.140, Q:S.140, Q:G.143, Q:G.144, Q:T.145, Q:T.145, Q:V.177, Q:E.183, Q:N.206, Q:N.206, Q:N.228 pi-Stacking: Q:Y.224, Q:Y.224 pi-Cation interactions: Q:Y.224 Salt bridges: P:K.252, P:K.252

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

GDP.2: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:G.144, B:S.176, B:S.176, B:E.181, B:N.204, B:N.204, B:N.226 pi-Cation interactions: B:Y.222 GDP.5: 17 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:S.138, D:G.142, D:T.143, D:G.144, D:S.176, D:S.176, D:E.181, D:N.204, D:N.204, D:N.226 pi-Cation interactions: D:Y.222 GDP.8: 16 residues within 4Å: Chain F: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Q.11, F:Q.11, F:C.12, F:S.138, F:G.142, F:T.143, F:G.144, F:S.176, F:S.176, F:E.181, F:N.204, F:N.204, F:N.226 pi-Cation interactions: F:Y.222 GDP.11: 17 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:C.12, H:S.138, H:G.142, H:T.143, H:G.144, H:S.176, H:S.176, H:E.181, H:N.204, H:N.204, H:N.226 pi-Cation interactions: H:Y.222 GDP.14: 17 residues within 4Å: Chain J: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:Q.11, J:Q.11, J:C.12, J:S.138, J:G.142, J:T.143, J:G.144, J:S.176, J:S.176, J:E.181, J:N.204, J:N.204, J:N.226 pi-Cation interactions: J:Y.222 GDP.17: 17 residues within 4Å: Chain L: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:Q.11, L:Q.11, L:C.12, L:S.138, L:G.142, L:T.143, L:G.144, L:S.176, L:S.176, L:E.181, L:N.204, L:N.204, L:N.226 pi-Cation interactions: L:Y.222 GDP.20: 17 residues within 4Å: Chain N: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain N Hydrogen bonds: N:Q.11, N:Q.11, N:C.12, N:S.138, N:G.142, N:T.143, N:G.144, N:S.176, N:S.176, N:E.181, N:N.204, N:N.204, N:N.226 pi-Cation interactions: N:Y.222 GDP.23: 17 residues within 4Å: Chain P: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:Q.11, P:Q.11, P:C.12, P:S.138, P:G.142, P:T.143, P:G.144, P:S.176, P:S.176, P:E.181, P:N.204, P:N.204, P:Y.222, P:N.226 pi-Cation interactions: P:Y.222 GDP.26: 17 residues within 4Å: Chain R: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain R Hydrogen bonds: R:Q.11, R:Q.11, R:C.12, R:S.138, R:G.142, R:T.143, R:G.144, R:S.176, R:S.176, R:E.181, R:N.204, R:N.204, R:N.226 pi-Cation interactions: R:Y.222

9 x YGY: Cryptophycin 52(Non-covalent)

YGY.3: 20 residues within 4Å: Chain A: E.254, T.257, N.258, P.261, M.313, W.346, C.347, P.348, T.349, K.352 Chain B: A.97, G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:K.103, B:T.178, B:V.179, B:V.180, B:F.394, B:F.394, B:W.397, A:E.254, A:T.257 Hydrogen bonds: B:N.100, B:V.179, A:T.257, A:N.258, A:K.352 YGY.6: 20 residues within 4Å: Chain C: E.254, T.257, N.258, P.261, M.313, W.346, C.347, P.348, 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 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:E.254, C:T.257, D:K.103, D:T.178, D:V.179, D:V.180, D:F.394, D:F.394, D:W.397 Hydrogen bonds: C:T.257, C:N.258, C:K.352, D:N.100, D:V.179 YGY.9: 21 residues within 4Å: Chain E: E.254, T.257, N.258, P.261, M.313, W.346, C.347, P.348, T.349, K.352 Chain F: A.97, G.98, N.99, N.100, K.103, D.177, T.178, V.179, V.180, F.394, W.397 13 PLIP interactions: 8 interactions with chain F, 5 interactions with chain E Hydrophobic interactions: F:K.103, F:T.178, F:V.179, F:V.180, F:F.394, F:W.397, E:E.254, E:T.257 Hydrogen bonds: F:N.100, F:V.179, E:T.257, E:N.258, E:K.352 YGY.12: 20 residues within 4Å: Chain G: E.254, T.257, N.258, P.261, M.313, W.346, C.347, P.348, 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 14 PLIP interactions: 5 interactions with chain G, 9 interactions with chain H Hydrophobic interactions: G:E.254, G:T.257, H:K.103, H:T.178, H:V.179, H:V.180, H:F.394, H:F.394, H:W.397 Hydrogen bonds: G:T.257, G:N.258, G:K.352, H:N.100, H:V.179 YGY.15: 20 residues within 4Å: Chain I: E.254, T.257, N.258, P.261, M.313, W.346, C.347, P.348, T.349, K.352 Chain J: A.97, G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 14 PLIP interactions: 9 interactions with chain J, 5 interactions with chain I Hydrophobic interactions: J:K.103, J:T.178, J:V.179, J:V.180, J:F.394, J:F.394, J:W.397, I:E.254, I:T.257 Hydrogen bonds: J:N.100, J:V.179, I:T.257, I:N.258, I:K.352 YGY.18: 20 residues within 4Å: Chain K: E.254, T.257, N.258, P.261, M.313, W.346, C.347, P.348, 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 14 PLIP interactions: 9 interactions with chain L, 5 interactions with chain K Hydrophobic interactions: L:K.103, L:T.178, L:V.179, L:V.180, L:F.394, L:F.394, L:W.397, K:E.254, K:T.257 Hydrogen bonds: L:N.100, L:V.179, K:T.257, K:N.258, K:K.352 YGY.21: 20 residues within 4Å: Chain M: E.254, T.257, N.258, P.261, M.313, W.346, C.347, P.348, T.349, K.352 Chain N: A.97, G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 14 PLIP interactions: 9 interactions with chain N, 5 interactions with chain M Hydrophobic interactions: N:K.103, N:T.178, N:V.179, N:V.180, N:F.394, N:F.394, N:W.397, M:E.254, M:T.257 Hydrogen bonds: N:N.100, N:V.179, M:T.257, M:N.258, M:K.352 YGY.24: 20 residues within 4Å: Chain O: E.254, T.257, N.258, P.261, M.313, W.346, C.347, P.348, 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 14 PLIP interactions: 5 interactions with chain O, 9 interactions with chain P Hydrophobic interactions: O:E.254, O:T.257, P:K.103, P:T.178, P:V.179, P:V.180, P:F.394, P:F.394, P:W.397 Hydrogen bonds: O:T.257, O:N.258, O:K.352, P:N.100, P:V.179 YGY.27: 20 residues within 4Å: Chain Q: E.254, T.257, N.258, P.261, M.313, W.346, C.347, P.348, T.349, K.352 Chain R: A.97, G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 14 PLIP interactions: 5 interactions with chain Q, 9 interactions with chain R Hydrophobic interactions: Q:E.254, Q:T.257, R:K.103, R:T.178, R:V.179, R:V.180, R:F.394, R:F.394, R:W.397 Hydrogen bonds: Q:T.257, Q:N.258, Q:K.352, R:N.100, R:V.179

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: ACEGIKMOQ
Tubulin beta-6 chain: BDFHJLNPR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
I

G
M

I
Q

K
U

M
Y

O
c

Q
g

B
B

D
F

F
J

H
N

J
R

L
V

N
Z

P
d

R
h

Detyrosinated tubulin alpha-1A chain

Tubulin beta-6 chain

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