SMTL ID : 9duq.1

HURP(65-174) bound to GMPCPP-stabilized microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-9-9-9-mer

Ligands

9 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

G2P.1: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Ligands: MG.2 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain K Hydrogen bonds: B:Q.11, B:C.12, B:E.69, B:A.97, B:G.98, B:N.99, B:N.99, B:S.138, B:G.141, B:G.142, B:T.143, B:T.143, B:G.144, B:D.177, B:N.204, B:N.204, B:N.226, B:N.226, K:E.254 pi-Stacking: B:Y.222, B:Y.222 pi-Cation interactions: B:Y.222 G2P.5: 19 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Chain I: L.248, E.254 Ligands: MG.6 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain I Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:A.97, D:N.99, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:D.177, D:N.204, D:N.204, D:N.226, D:N.226, I:E.254 pi-Stacking: D:Y.222, D:Y.222 G2P.9: 21 residues within 4Å: Chain F: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Chain M: L.248, E.254 Ligands: MG.10 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:Q.11, F:C.12, F:A.97, F:N.99, F:N.99, F:S.138, F:G.142, F:T.143, F:T.143, F:G.144, F:D.177, F:N.204, F:N.204, F:N.226, F:N.226 pi-Stacking: F:Y.222, F:Y.222 G2P.13: 17 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Ligands: MG.14 18 PLIP interactions: 18 interactions with chain H Hydrogen bonds: H:Q.11, H:C.12, H:A.97, H:G.98, H:N.99, H:S.138, H:G.142, H:T.143, H:T.143, H:G.144, H:D.177, H:N.204, H:N.226, H:N.226, H:N.226 pi-Stacking: H:Y.222, H:Y.222 pi-Cation interactions: H:Y.222 G2P.17: 19 residues within 4Å: Chain J: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 Ligands: MG.18 20 PLIP interactions: 20 interactions with chain J Hydrogen bonds: J:Q.11, J:Q.11, J:C.12, J:A.97, J:N.99, J:S.138, J:G.141, J:G.142, J:T.143, J:T.143, J:G.144, J:D.177, J:D.177, J:E.181, J:E.181, J:N.204, J:N.204, J:N.226, J:N.226 pi-Cation interactions: J:Y.222 G2P.21: 19 residues within 4Å: Chain L: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, L.225, N.226 Ligands: MG.22 16 PLIP interactions: 16 interactions with chain L Hydrogen bonds: L:Q.11, L:C.12, L:A.97, L:N.99, L:S.138, L:G.142, L:T.143, L:T.143, L:G.144, L:E.181, L:N.204, L:N.204, L:N.226, L:N.226 pi-Stacking: L:Y.222, L:Y.222 G2P.25: 18 residues within 4Å: Chain E: L.248, E.254 Chain N: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Ligands: MG.26 22 PLIP interactions: 1 interactions with chain E, 21 interactions with chain N Hydrogen bonds: E:E.254, N:Q.11, N:Q.11, N:C.12, N:A.97, N:G.98, N:N.99, N:N.99, N:S.138, N:G.142, N:T.143, N:T.143, N:G.144, N:D.177, N:D.177, N:N.204, N:N.204, N:N.226, N:N.226 pi-Stacking: N:Y.222, N:Y.222 pi-Cation interactions: N:Y.222 G2P.29: 18 residues within 4Å: Chain C: L.248 Chain P: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Ligands: MG.30 20 PLIP interactions: 20 interactions with chain P Hydrogen bonds: P:Q.11, P:Q.11, P:Q.11, P:C.12, P:A.97, P:N.99, P:S.138, P:G.142, P:T.143, P:T.143, P:G.144, P:D.177, P:D.177, P:N.204, P:N.204, P:N.226, P:N.226 pi-Stacking: P:Y.222, P:Y.222 pi-Cation interactions: P:Y.222 G2P.33: 20 residues within 4Å: Chain G: L.248, E.254 Chain R: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Ligands: MG.34 19 PLIP interactions: 2 interactions with chain G, 17 interactions with chain R Hydrogen bonds: G:E.254, G:E.254, R:Q.11, R:Q.11, R:C.12, R:N.99, R:S.138, R:G.142, R:T.143, R:T.143, R:G.144, R:D.177, R:D.177, R:N.204, R:N.204, R:N.226, R:N.226 pi-Stacking: R:Y.222, R:Y.222

18 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain B: E.69 Ligands: G2P.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.69 MG.4: 4 residues within 4Å: Chain B: K.252 Chain C: E.71, D.98 Ligands: GTP.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.71, C:D.98 MG.6: 1 residues within 4Å: Ligands: G2P.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: K.252 Chain E: E.71 Ligands: GTP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.71 MG.10: 2 residues within 4Å: Chain F: E.69 Ligands: G2P.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.69 MG.12: 3 residues within 4Å: Chain G: E.71, D.98 Ligands: GTP.11 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.71, G:D.98 MG.14: 1 residues within 4Å: Ligands: G2P.13 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain H: K.252 Chain I: E.71 Ligands: GTP.15 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:E.71 MG.18: 3 residues within 4Å: Chain J: E.69, T.143 Ligands: G2P.17 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:E.69 MG.20: 3 residues within 4Å: Chain J: K.252 Chain K: E.71 Ligands: GTP.19 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:E.71, K:E.71 MG.22: 2 residues within 4Å: Chain L: E.69 Ligands: G2P.21 No protein-ligand interaction detected (PLIP) MG.24: 5 residues within 4Å: Chain L: K.252 Chain M: Q.11, E.71, D.98 Ligands: GTP.23 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:E.71 MG.26: 1 residues within 4Å: Ligands: G2P.25 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain N: K.252 Chain O: Q.11, E.71 Ligands: GTP.27 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:E.71 MG.30: 2 residues within 4Å: Chain P: T.143 Ligands: G2P.29 No protein-ligand interaction detected (PLIP) MG.32: 5 residues within 4Å: Chain P: K.252 Chain Q: Q.11, E.71, D.98 Ligands: GTP.31 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:E.71 MG.34: 1 residues within 4Å: Ligands: G2P.33 No protein-ligand interaction detected (PLIP) MG.36: 4 residues within 4Å: Chain S: Q.11, E.71, D.98 Ligands: GTP.35 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:E.71

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

GTP.3: 26 residues within 4Å: Chain B: L.246, K.252 Chain C: G.10, Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.4 25 PLIP interactions: 3 interactions with chain B, 22 interactions with chain C Salt bridges: B:K.252, B:K.252, B:K.252 Hydrogen bonds: C:Q.11, C:A.12, C:Q.15, C:D.98, C:A.99, C:A.100, C:N.101, C:S.140, C:G.143, C:G.144, C:T.145, C:T.145, C:G.146, C:E.183, C:N.206, C:N.206, C:Y.224, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 pi-Cation interactions: C:Y.224 GTP.7: 26 residues within 4Å: Chain D: Q.245, L.246, K.252 Chain E: G.10, Q.11, A.12, Q.15, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.8 21 PLIP interactions: 1 interactions with chain D, 20 interactions with chain E Salt bridges: D:K.252 Hydrogen bonds: E:Q.11, E:A.12, E:Q.15, E:A.99, E:A.100, E:N.101, E:S.140, E:G.144, E:T.145, E:T.145, E:T.145, E:G.146, 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 GTP.11: 24 residues within 4Å: Chain F: K.252 Chain G: G.10, Q.11, A.12, Q.15, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.12 20 PLIP interactions: 17 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:Q.11, G:A.12, G:Q.15, G:N.101, G:S.140, G:G.144, G:T.145, G:T.145, G:G.146, 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: F:K.252, F:K.252, F:K.252 GTP.15: 26 residues within 4Å: Chain H: L.246, K.252 Chain I: G.10, Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.16 17 PLIP interactions: 16 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:Q.11, I:A.12, I:Q.15, I:N.101, I:N.101, I:S.140, I:G.144, I:T.145, I:T.145, I:G.146, I:E.183, I:N.206, I:N.206, I:N.228, I:N.228 pi-Cation interactions: I:Y.224 Salt bridges: H:K.252 GTP.19: 24 residues within 4Å: Chain J: L.246, K.252 Chain K: 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, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.20 19 PLIP interactions: 16 interactions with chain K, 3 interactions with chain J Hydrogen bonds: K:Q.11, K:A.12, K:A.99, K:A.100, K:N.101, K:S.140, K:G.144, K:T.145, K:T.145, K:G.146, K:E.183, K:N.206, K:N.206, K:N.228, K:N.228 pi-Cation interactions: K:Y.224 Salt bridges: J:K.252, J:K.252, J:K.252 GTP.23: 25 residues within 4Å: Chain L: K.252 Chain M: G.10, Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.24 20 PLIP interactions: 17 interactions with chain M, 3 interactions with chain L Hydrogen bonds: M:Q.11, M:A.12, M:Q.15, M:N.101, M:S.140, M:G.144, M:T.145, M:T.145, M:G.146, 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: L:K.252, L:K.252, L:K.252 GTP.27: 24 residues within 4Å: Chain N: L.246, K.252 Chain O: G.10, Q.11, A.12, Q.15, D.69, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Ligands: MG.28 20 PLIP interactions: 17 interactions with chain O, 3 interactions with chain N Hydrogen bonds: O:Q.11, O:A.12, O:Q.15, O:A.99, O:N.101, O:S.140, O:G.144, O:T.145, O:T.145, O:G.146, 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: N:K.252, N:K.252, N:K.252 GTP.31: 26 residues within 4Å: Chain P: L.246, K.252 Chain Q: G.10, Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.32 21 PLIP interactions: 20 interactions with chain Q, 1 interactions with chain P Hydrogen bonds: Q:Q.11, Q:A.12, Q:Q.15, Q:D.98, Q:A.99, Q:A.100, Q:N.101, Q:S.140, Q:G.144, Q:T.145, Q:T.145, Q:G.146, Q:E.183, Q:N.206, Q:N.206, Q:N.228, Q:N.228 pi-Stacking: Q:Y.224, Q:Y.224 pi-Cation interactions: Q:Y.224 Salt bridges: P:K.252 GTP.35: 23 residues within 4Å: Chain R: K.252 Chain S: G.10, Q.11, A.12, Q.15, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.36 20 PLIP interactions: 18 interactions with chain S, 2 interactions with chain R Hydrogen bonds: S:Q.11, S:A.12, S:Q.15, S:D.98, S:A.100, S:N.101, S:S.140, S:G.144, S:T.145, S:T.145, S:G.146, S:N.206, S:N.206, S:N.228, S:N.228 pi-Stacking: S:Y.224, S:Y.224 pi-Cation interactions: S:Y.224 Salt bridges: R:K.252, R:K.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valdez, V.A. et al., HURP facilitates spindle assembly by stabilizing microtubules and working synergistically with TPX2. Nat Commun (2024)

Release Date

2024-11-27

Peptides

Disks large-associated protein 5: ATUVWXYZ0
Tubulin beta chain: BDFHJLNPR
Tubulin alpha chain: CEGIKMOQS

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
r

T
s

U
t

V
u

W
v

X
w

Y
x

Z
y

0
z

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

R
R

C
A

E
C

G
E

I
G

K
I

M
K

O
M

Q
O

S
Q

Disks large-associated protein 5

Tubulin beta chain

Tubulin alpha chain

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