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SMTL ID : 5itz.1

Crystal structure of the SAC domain of CPAP in a complex with Tubulin and Darpin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

GTP.1:

26 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.142, G.143, G.144, T.145, G.146, I.171, P.173, V.177, S.178, E.183, N.206, Y.224, N.228, I.231
Chain B: K.252
Ligands: MG.2

29 PLIP interactions:

26 interactions with chain A, 3 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:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:S.178, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228
Water bridges: A:G.13, A:D.98, A:D.98, A:D.98, A:F.141, B:K.252, B:K.252
pi-Stacking: A:Y.224, A:Y.224
Salt bridges: B:K.252

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2:

1 residues within 4Å:

Ligands: GTP.1

No protein-ligand interaction detected (PLIP)

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

GDP.3:

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, L.207, Y.222, N.226

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:E.181, B:N.204, B:N.204, B:N.226, B:N.226
Water bridges: B:Q.11, B:Q.11, B:G.13, B:D.67, B:L.139, B:G.141, B:G.141, B:T.143, B:S.176
pi-Stacking: B:Y.222, B:Y.222

1 x LOC: N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide(Non-covalent)

LOC.4:

20 residues within 4Å:

Chain A: S.178, T.179, A.180, V.181
Chain B: C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, I.316, N.348, K.350, I.368

9 PLIP interactions:

8 interactions with chain B, 1 interactions with chain A

Hydrophobic interactions: B:A.248, B:K.252, B:L.253, B:N.256, B:A.314, B:K.350, B:K.350
Water bridges: B:C.239
Hydrogen bonds: A:V.181

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sharma, A. et al., Centriolar CPAP/SAS-4 Imparts Slow Processive Microtubule Growth. Dev.Cell (2016)

Release Date

2016-06-01

Peptides

Tubulin alpha-1B chain: A
Tubulin beta-2B chain: B
Centromere protein J: C
Designed ankyrin repeat protein (DARPIN) D1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
F

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Tubulin alpha-1B chain

Tubulin beta-2B chain

Centromere protein J

Designed ankyrin repeat protein (DARPIN) D1

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
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High
Extreme

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